In jranke/mkin: Kinetic Evaluation of Chemical Degradation Data

Introduction

In this document, the example evaluations provided in Attachment 1 to the SOP of US EPA for using the NAFTA guidance [@usepa2015] are repeated using mkin. The original evaluations reported in the attachment were performed using PestDF in version 0.8.4. Note that PestDF 0.8.13 is the version distributed at the US EPA website today (2019-02-26).

The datasets are now distributed with the mkin package.

library(knitr)
opts_chunk$set(tidy = FALSE, cache = FALSE, fig.height = 7)
library("mkin", quietly = TRUE)

Examples where DFOP did not converge with PestDF 0.8.4

In attachment 1, it is reported that the DFOP model does not converge for these datasets when PestDF 0.8.4 was used. For all four datasets, the DFOP model can be fitted with mkin (see below). The negative half-life given by PestDF 0.8.4 for these fits appears to be the result of a bug. The results for the other two models (SFO and IORE) are the same.

Example on page 5, upper panel

p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]])
plot(p5a)
print(p5a)

Example on page 5, lower panel

p5b <- nafta(NAFTA_SOP_Attachment[["p5b"]])
plot(p5b)
print(p5b)

Example on page 6

p6 <- nafta(NAFTA_SOP_Attachment[["p6"]])
plot(p6)
print(p6)

Example on page 7

p7 <- nafta(NAFTA_SOP_Attachment[["p7"]])
plot(p7)
print(p7)

Examples where the representative half-life deviates from the observed DT50

Example on page 8

For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.

p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent = 1e-3))
plot(p8)
print(p8)

Examples where SFO was not selected for an abiotic study

Example on page 9, upper panel

p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])
plot(p9a)
print(p9a)

In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.

Example on page 9, lower panel

p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
plot(p9b)
print(p9b)

Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.

Example on page 10

p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
plot(p10)
print(p10)

Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.

The DT50 was not observed during the study

Example on page 11

p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
plot(p11)
print(p11)

In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.

N is less than 1 and the DFOP rate constants are like the SFO rate constant

In the following three examples, the same results are obtained with mkin as reported for PestDF. As in the case on page 10, the N values below 1 are deemed unrealistic and appear to be the result of an overparameterisation.

Example on page 12, upper panel

p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])
plot(p12a)
print(p12a)

Example on page 12, lower panel

p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
plot(p12b)
print(p12b)

Example on page 13

p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
plot(p13)
print(p13)

DT50 not observed in the study and DFOP problems in PestDF

p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])
plot(p14)
print(p14)

The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.

N is less than 1 and DFOP fraction parameter is below zero

p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])
plot(p15a)
print(p15a)

p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
plot(p15b)
print(p15b)

In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.

The DFOP fraction parameter is greater than 1

p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])
plot(p16)
print(p16)

In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower $\chi^2$ error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.

Conclusions

The results obtained with mkin deviate from the results obtained with PestDF either in cases where one of the interpretive rules would apply, i.e. the IORE parameter N is less than one or the DFOP k values obtained with PestDF are equal to the SFO k values, or in cases where the DFOP model did not converge, which often lead to negative rate constants returned by PestDF.

Therefore, mkin appears to suitable for kinetic evaluations according to the NAFTA guidance.

References

jranke/mkin documentation built on April 29, 2024, 7:33 a.m.