From dd6c4a8f895fd470345e7ae773299daaa4de7aef Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 22 Feb 2019 20:51:13 +0100
Subject: Implement the NAFTA evaluation scheme

---
 man/NAFTA_2015_datasets.Rd | 35 +++++++++++++++++++++++++++++++++
 man/nafta.Rd               | 48 ++++++++++++++++++++++++++++++++++++++++++++++
 man/plot.nafta.Rd          | 31 ++++++++++++++++++++++++++++++
 man/print.nafta.Rd         | 22 +++++++++++++++++++++
 4 files changed, 136 insertions(+)
 create mode 100644 man/NAFTA_2015_datasets.Rd
 create mode 100644 man/nafta.Rd
 create mode 100644 man/plot.nafta.Rd
 create mode 100644 man/print.nafta.Rd

(limited to 'man')

diff --git a/man/NAFTA_2015_datasets.Rd b/man/NAFTA_2015_datasets.Rd
new file mode 100644
index 00000000..4ca494ee
--- /dev/null
+++ b/man/NAFTA_2015_datasets.Rd
@@ -0,0 +1,35 @@
+\name{NAFTA_2015_datasets}
+\alias{MRID_555555}
+\docType{data}
+\title{
+Example datasets from the NAFTA guidance published 2015
+}
+\description{
+Data taken from US EPA (2015), p. 23.
+}
+\usage{NAFTA_2015_datasets}
+\format{
+  1 dataset with observations on the following variables.
+  \describe{
+    \item{\code{name}}{a factor containing the name of the observed variable}
+    \item{\code{time}}{a numeric vector containing time points}
+    \item{\code{value}}{a numeric vector containing concentrations}
+  }
+}
+\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_evaluation <- nafta(MRID_555555)
+  print(nafta_evaluation)
+  plot(nafta_evaluation)
+}
+\keyword{datasets}
diff --git a/man/nafta.Rd b/man/nafta.Rd
new file mode 100644
index 00000000..cd06e02b
--- /dev/null
+++ b/man/nafta.Rd
@@ -0,0 +1,48 @@
+\name{nafta}
+\alias{nafta}
+\title{
+Evaluate parent kinetics using the NAFTA guidance
+}
+\usage{
+nafta(ds, title = NA, quiet = FALSE)
+}
+\description{
+  The function fits the SFO, IORE and DFOP models using
+  \code{\link{mmkin}} and returns an object of class
+  \code{nafta} that has methods for printing and plotting.
+}
+\arguments{
+  \item{ds}{
+    A dataframe that must contain one variable called "time" with the time
+    values specified by the \code{time} argument, one column called "name" with
+    the grouping of the observed values, and finally one column of observed
+    values called "value".
+  }
+  \item{title}{ Optional title of the dataset }
+  \item{quiet}{ Should the evaluation text be shown? }
+}
+\value{
+  An list of class \code{nafta}. The list element named "mmkin" is the
+  \code{\link{mmkin}} object containing the fits of the three models.
+  The list element named "title" contains the title of the dataset used.
+  The list element "data" contains the dataset used in the fits.
+}
+\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_evaluation <- nafta(MRID_555555)
+  print(nafta_evaluation)
+  plot(nafta_evaluation)
+}
+\author{
+  Johannes Ranke
+}
diff --git a/man/plot.nafta.Rd b/man/plot.nafta.Rd
new file mode 100644
index 00000000..a3dfdbae
--- /dev/null
+++ b/man/plot.nafta.Rd
@@ -0,0 +1,31 @@
+\name{plot.nafta}
+\alias{plot.nafta}
+\title{
+  Plot the results of the three models used in the NAFTA scheme
+}
+\description{
+  Calls \code{\link{plot.mmkin}}.
+}
+\usage{
+\method{plot}{nafta}(x, legend = FALSE, main = "auto", \dots)
+}
+\arguments{
+  \item{x}{
+    An object of class \code{\link{nafta}}.
+  }
+  \item{legend}{
+    Should a legend be added?
+  }
+  \item{main}{
+    Possibility to override the main title of the plot.
+  }
+  \item{\dots}{
+    Further arguments passed to \code{\link{plot.mmkin}}.
+  }
+}
+\value{
+  The function is called for its side effect.
+}
+\author{
+  Johannes Ranke
+}
diff --git a/man/print.nafta.Rd b/man/print.nafta.Rd
new file mode 100644
index 00000000..4ae4c8b2
--- /dev/null
+++ b/man/print.nafta.Rd
@@ -0,0 +1,22 @@
+\name{print.nafta}
+\alias{print.nafta}
+\title{
+  Print nafta objects
+}
+\description{
+  Print nafta objects.
+}
+\usage{
+  \method{print}{nafta}(x, quiet = TRUE, ...)
+}
+\arguments{
+  \item{x}{
+    An \code{\link{nafta}} object.
+  }
+  \item{quiet}{
+    Should the evaluation text be shown?
+  }
+  \item{\dots}{
+    Not used.
+  }
+}
-- 
cgit v1.2.1