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

6 files changed, 45 insertions, 6 deletions

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, ...)