mkin 0.9.44.9000

Summary method for class "mkinfit"

Usage

# 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.
x
an object of class summary.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
digits
Number of digits to use for printing
...
optional arguments passed to methods like print.

Description

Lists model equations, the summary as returned by summary.modFit, the chi2 error levels calculated according to FOCUS guidance (2006) as far as defined therein, and optionally the data, consisting of observed, predicted and residual values.

Value

The summary function returns a list derived from summary.modFit, 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

use_of_ff
Was maximum or minimum use made of formation fractions

residuals, residualVariance, sigma, modVariance, df
As in summary.modFit

cov.unscaled, cov.scaled, info, niter, stopmess, par
As in summary.modFit

bpar
Optimised and backtransformed parameters

diffs
The differential equations used in the model

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.

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.

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://focus.jrc.ec.europa.eu/dk

Examples

  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))


mkin version:    0.9.44.9000 
R version:       3.3.1 
Date of fit:     Sat Sep 10 05:53:12 2016 
Date of summary: Sat Sep 10 05:53:12 2016 

Equations:
d_parent = - k_parent_sink * parent

Model predictions using solution type analytical 

Fitted with method Port using 35 model solutions performed in 0.09 s

Weighting: none

Starting values for parameters to be optimised:
               value   type
parent_0      101.24  state
k_parent_sink   0.10 deparm

Starting values for the transformed parameters actually optimised:
                       value lower upper
parent_0          101.240000  -Inf   Inf
log_k_parent_sink  -2.302585  -Inf   Inf

Fixed parameter values:
None

Optimised, transformed parameters with symmetric confidence intervals:
                  Estimate Std. Error  Lower   Upper
parent_0           109.200     4.3910 98.410 119.900
log_k_parent_sink   -3.291     0.1152 -3.573  -3.009

Parameter correlation:
                  parent_0 log_k_parent_sink
parent_0             1.000             0.575
log_k_parent_sink    0.575             1.000

Residual standard error: 6.08 on 6 degrees of freedom

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  24.860 1.394e-07 98.41000 119.90000
k_parent_sink   0.03722   8.679 6.457e-05  0.02807   0.04934

Chi2 error levels in percent:
         err.min n.optim df
All data   8.385       2  6
parent     8.385       2  6

Resulting formation fractions:
            ff
parent_sink  1

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

Author

Johannes Ranke