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