From 396e40d2c45d81a8e74c41a2f632665021e980a1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 26 Feb 2019 20:28:15 +0100 Subject: NAFTA SOP Attachment vignette Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0 --- man/AIC.mmkin.Rd | 2 +- man/NAFTA_SOP_2015.Rd | 2 +- man/NAFTA_SOP_Attachment.Rd | 31 +++++++++++++++++++++++++++++++ man/nafta.Rd | 8 ++++++-- man/plot.nafta.Rd | 4 +++- man/print.nafta.Rd | 4 +++- 6 files changed, 45 insertions(+), 6 deletions(-) create mode 100644 man/NAFTA_SOP_Attachment.Rd (limited to 'man') diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd index e7f5c228..08e4cc57 100644 --- a/man/AIC.mmkin.Rd +++ b/man/AIC.mmkin.Rd @@ -28,7 +28,7 @@ \examples{ f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS A" = FOCUS_2006_A, - "FOCUS C" = FOCUS_2006_C)) + "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE) AIC(f[1, "FOCUS A"]) # We get a single number for a single fit # For FOCUS A, the models fit almost equally well, so the higher the number diff --git a/man/NAFTA_SOP_2015.Rd b/man/NAFTA_SOP_2015.Rd index a47ae155..bca4cba2 100644 --- a/man/NAFTA_SOP_2015.Rd +++ b/man/NAFTA_SOP_2015.Rd @@ -29,7 +29,7 @@ Data taken from US EPA (2015), p. 19 and 23. \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} } \examples{ - nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D) + nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1) print(nafta_evaluation) plot(nafta_evaluation) } diff --git a/man/NAFTA_SOP_Attachment.Rd b/man/NAFTA_SOP_Attachment.Rd new file mode 100644 index 00000000..b8d015a4 --- /dev/null +++ b/man/NAFTA_SOP_Attachment.Rd @@ -0,0 +1,31 @@ +\name{NAFTA_SOP_Attachment} +\alias{NAFTA_SOP_Attachment} +\docType{data} +\title{ +Example datasets from Attachment 1 to the NAFTA SOP published 2015 +} +\description{ +Data taken from from Attachment 1 of the SOP. +} +\usage{NAFTA_SOP_Attachment} +\format{ + Additionally, a list (NAFTA_SOP_Attachment) containing 16 datasets suitable + for the evaluation with \code{\link{nafta}} +} +\source{ + NAFTA (2011) Guidance for evaluating and calculating degradation kinetics + in environmental media. NAFTA Technical Working Group on Pesticides + \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} + accessed 2019-02-22 + + US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to + Calculate Representative Half-life Values and Characterizing Pesticide + Degradation + \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} +} +\examples{ + nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1) + print(nafta_att_p5a) + plot(nafta_att_p5a) +} +\keyword{datasets} diff --git a/man/nafta.Rd b/man/nafta.Rd index 48b4fefe..6917d0e9 100644 --- a/man/nafta.Rd +++ b/man/nafta.Rd @@ -4,7 +4,7 @@ Evaluate parent kinetics using the NAFTA guidance } \usage{ -nafta(ds, title = NA, quiet = FALSE) +nafta(ds, title = NA, quiet = FALSE, \dots) } \description{ The function fits the SFO, IORE and DFOP models using @@ -20,6 +20,10 @@ nafta(ds, title = NA, quiet = FALSE) } \item{title}{ Optional title of the dataset } \item{quiet}{ Should the evaluation text be shown? } + \item{\dots}{ + Further arguments passed to \code{\link{mmkin}}. + } + } \value{ An list of class \code{nafta}. The list element named "mmkin" is the @@ -39,7 +43,7 @@ nafta(ds, title = NA, quiet = FALSE) \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} } \examples{ - nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D) + nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1) print(nafta_evaluation) plot(nafta_evaluation) } diff --git a/man/plot.nafta.Rd b/man/plot.nafta.Rd index a3dfdbae..62bbcddf 100644 --- a/man/plot.nafta.Rd +++ b/man/plot.nafta.Rd @@ -1,7 +1,9 @@ \name{plot.nafta} \alias{plot.nafta} \title{ - Plot the results of the three models used in the NAFTA scheme + Plot the results of the three models used in the NAFTA scheme. The plots + are ordered with increasing complexity of the model in this function + (SFO, then IORE, then DFOP). } \description{ Calls \code{\link{plot.mmkin}}. diff --git a/man/print.nafta.Rd b/man/print.nafta.Rd index 4ae4c8b2..78ece0ad 100644 --- a/man/print.nafta.Rd +++ b/man/print.nafta.Rd @@ -4,7 +4,9 @@ Print nafta objects } \description{ - Print nafta objects. + Print nafta objects. The results for the three models + are printed in the order of increasing model complexity, + i.e. SFO, then IORE, and finally DFOP. } \usage{ \method{print}{nafta}(x, quiet = TRUE, ...) -- cgit v1.2.1