From 91a5834dd701211f929fd25419dc34561ce3b4e7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Feb 2025 09:15:20 +0100 Subject: Initialize dev docs --- docs/dev/reference/summary.mkinfit.html | 290 ++++++++++++++++++++++++++++++++ 1 file changed, 290 insertions(+) create mode 100644 docs/dev/reference/summary.mkinfit.html (limited to 'docs/dev/reference/summary.mkinfit.html') diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html new file mode 100644 index 00000000..63a08d05 --- /dev/null +++ b/docs/dev/reference/summary.mkinfit.html @@ -0,0 +1,290 @@ + +Summary method for class "mkinfit" — summary.mkinfit • mkin + Skip to contents + + +
+
+
+ +

Summary method for class "mkinfit"

+ Source: R/summary.mkinfit.R +
summary.mkinfit.Rd
+
+ +
+

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.

+
+ +
+

Usage

+ 
# S3 method for class 'mkinfit'
+summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
+
+# S3 method for class '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 +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

+
+
+

Author

+

Johannes Ranke

+
+ +
+

Examples

+ 

+  summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
+#> mkin version used for fitting:    1.2.10 
+#> R version used for fitting:       4.4.2 
+#> Date of fit:     Fri Feb 14 07:34:16 2025 
+#> Date of summary: Fri Feb 14 07:34:16 2025 
+#> 
+#> 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
+
+
+
+
+ + +
+ + + + + + + -- cgit v1.2.1