mkindsg class to hold groups of datasets

- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU
  assessment as mkindsg object with metadata
- f_time_norm_focus() to do time-step normalisation using the FOCUS
  method
- focus_soil_moisture data with default moisture contents at pF1,
  pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance
- Dataset generation scripts in inst/dataset_generation
- Depend on R >= 2.15.1 in order to facilitate the use of
  utils::globalVariables()

7 files changed, 253 insertions, 23 deletions

diff --git a/man/D24_2014.Rd b/man/D24_2014.Rd
new file mode 100644
index 00000000..90b0605e
--- /dev/null
+++ b/man/D24_2014.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/D24_2014.R
+\docType{data}
+\name{D24_2014}
+\alias{D24_2014}
+\title{Aerobic soil degradation data on 2,4-D from the EU assessment in 2014}
+\format{
+An \link{mkindsg} object grouping five datasets
+}
+\source{
+Hellenic Ministry of Rural Development and Agriculture (2014)
+Final addendum to the Renewal Assessment Report - public version - 2,4-D
+Volume 3 Annex B.8 Fate and behaviour in the environment p. 638, 640,
+644-646.
+\url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812}
+}
+\usage{
+D24_2014
+}
+\description{
+The five datasets were extracted from the active substance evaluation dossier
+published by EFSA. Kinetic evaluations shown for these datasets are intended
+to illustrate and advance kinetic modelling. The fact that these data and
+some results are shown here does not imply a license to use them in the
+context of pesticide  registrations, as the use of the data may be
+constrained by data protection regulations.
+}
+\details{
+Metabolite residues at early sampling times reported as 0.0 were set to NA.
+
+The R code used to create this data object is installed with this package
+in the 'dataset_generation' directory. In the code, page numbers are given for
+specific pieces of information in the comments.
+}
+\examples{
+print(D24_2014)
+print(D24_2014$ds[[1]], data = TRUE)
+m1 = mkinmod(D24 = list(type = "SFO", to = "phenol"),
+  phenol = list(type = "SFO", to = "anisole"),
+  anisole = list(type = "SFO"))
+}
+\keyword{datasets}
diff --git a/man/experimental_data_for_UBA.Rd b/man/experimental_data_for_UBA.Rd
index e3386a2f..e28f15d2 100644
--- a/man/experimental_data_for_UBA.Rd
+++ b/man/experimental_data_for_UBA.Rd
@@ -30,12 +30,12 @@
  (Austria, 2015, p. 16).
 
  Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
- (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling,
  the residues given for the metabolite were added to the parent
  value, following the recommendation of the FOCUS kinetics workgroup.
 
  Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
- (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ (Hellas, 2013, p. 644). Values reported as zero were set to NA, with
  the exception of the day three sampling of metabolite A2, which was set
  to one half of the LOD reported to be 1\% AR.
 
@@ -66,10 +66,10 @@
   Version 1.1, 18 December 2014
   \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 
-  Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
+  Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
   and Behaviour
 
-  Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
+  Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
   environment
 
   Ranke (2019) Documentation of results obtained for the error model expertise
diff --git a/man/f_time_norm_focus.Rd b/man/f_time_norm_focus.Rd
new file mode 100644
index 00000000..9d858312
--- /dev/null
+++ b/man/f_time_norm_focus.Rd
@@ -0,0 +1,72 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/f_time_norm_focus.R
+\name{f_time_norm_focus}
+\alias{f_time_norm_focus}
+\alias{f_time_norm_focus.numeric}
+\alias{f_time_norm_focus.mkindsg}
+\title{Normalisation factors for aerobic soil degradation according to FOCUS guidance}
+\usage{
+f_time_norm_focus(object, ...)
+
+\method{f_time_norm_focus}{numeric}(
+  object,
+  moisture = NA,
+  field_moisture = NA,
+  temperature = object,
+  Q10 = 2.58,
+  walker = 0.7,
+  f_na = NA,
+  ...
+)
+
+\method{f_time_norm_focus}{mkindsg}(object, Q10 = 2.58, walker = 0.7, f_na = NA, ...)
+}
+\arguments{
+\item{object}{An object containing information used for the calculations}
+
+\item{\dots}{Currently not used}
+
+\item{moisture}{Numeric vector of moisture contents in \\\% w/w}
+
+\item{field_moisture}{Numeric vector of moisture contents at field capacity
+(pF2) in \\\% w/w}
+
+\item{temperature}{Numeric vector of temperatures in °C}
+
+\item{Q10}{The Q10 value used for temperature normalisation}
+
+\item{walker}{The Walker exponent used for moisture normalisation}
+
+\item{f_na}{The factor to use for NA values. If set to NA, only factors
+for complete cases will be returned.}
+}
+\description{
+Time step normalisation factors for aerobic soil degradation as described
+in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).
+}
+\examples{
+f_time_norm_focus(25, 20, 25) # 1.37, compare p. 184
+
+D24_2014$meta
+# No moisture normalisation in the first dataset, so we use f_na = 1 to get
+# Temperature only normalisation as in the EU evaluation
+f_time_norm_focus(D24_2014, f_na = 1)
+# Moisture normalisation for the other four soils is one, as soil moisture
+# is higher than the approximate field capacity derived from the USDA soil
+# type
+}
+\references{
+FOCUS (2006) \dQuote{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,
+\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+Version 1.1, 18 December 2014
+\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
+\seealso{
+\link{focus_soil_moisture}
+}
diff --git a/man/focus_soil_moisture.Rd b/man/focus_soil_moisture.Rd
new file mode 100644
index 00000000..015dd261
--- /dev/null
+++ b/man/focus_soil_moisture.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/focus_soil_moisture.R
+\docType{data}
+\name{focus_soil_moisture}
+\alias{focus_soil_moisture}
+\title{FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar}
+\format{
+A matrix with upper case USDA soil classes as row names, and water tension
+('pF1', 'pF2', 'pF 2.5') as column names
+}
+\source{
+Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment
+Version 2.2, May 2014 \url{https://esdac.jrc.ec.europa.eu/projects/ground-water}
+}
+\usage{
+focus_soil_moisture
+}
+\description{
+FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar
+}
+\examples{
+focus_soil_moisture
+}
+\keyword{datasets}
diff --git a/man/mkinds.Rd b/man/mkinds.Rd
index 8d1860e8..4bdd39bb 100644
--- a/man/mkinds.Rd
+++ b/man/mkinds.Rd
@@ -2,7 +2,18 @@
 % Please edit documentation in R/mkinds.R
 \name{mkinds}
 \alias{mkinds}
+\alias{print.mkinds}
 \title{A dataset class for mkin}
+\usage{
+\method{print}{mkinds}(x, data = FALSE, ...)
+}
+\arguments{
+\item{x}{An \link{mkinds} object.}
+
+\item{data}{Should the data be printed?}
+
+\item{\dots}{Not used.}
+}
 \description{
 At the moment this dataset class is hardly used in mkin. For example,
 mkinfit does not take mkinds datasets as argument, but works with dataframes
@@ -15,9 +26,6 @@ mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
 print(mds)
 
 }
-\seealso{
-The S3 printing method \code{\link{print.mkinds}}
-}
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
 \describe{
diff --git a/man/mkindsg.Rd b/man/mkindsg.Rd
new file mode 100644
index 00000000..919d3bb9
--- /dev/null
+++ b/man/mkindsg.Rd
@@ -0,0 +1,100 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinds.R
+\name{mkindsg}
+\alias{mkindsg}
+\alias{print.mkindsg}
+\title{A class for dataset groups for mkin}
+\usage{
+\method{print}{mkindsg}(x, data = FALSE, verbose = data, ...)
+}
+\arguments{
+\item{x}{An \link{mkindsg} object.}
+
+\item{data}{Should the mkinds objects be printed with their data?}
+
+\item{verbose}{Should the mkinds objects be printed?}
+
+\item{\dots}{Not used.}
+}
+\description{
+A container for working with datasets that share at least one compound,
+so that combined evaluations are desirable.
+
+Time normalisation factors are initialised with a value of 1 for each
+dataset if no data are supplied.
+}
+\examples{
+
+mdsg <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])
+print(mdsg)
+print(mdsg, verbose = TRUE)
+print(mdsg, verbose = TRUE, data = TRUE)
+
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{title}}{A title for the dataset group}
+
+\item{\code{ds}}{A list of mkinds objects}
+
+\item{\code{observed_n}}{Occurrence counts of compounds in datasets}
+
+\item{\code{f_time_norm}}{Time normalisation factors}
+
+\item{\code{meta}}{A data frame with a row for each dataset,
+containing additional information in the form
+of categorical data (factors) or numerical data
+(e.g. temperature, moisture,
+or covariates like soil pH).}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{mkindsg$new()}}
+\item \href{#method-clone}{\code{mkindsg$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+Create a new mkindsg object
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{mkindsg$new(title = "", ds, f_time_norm = rep(1, length(ds)), meta)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{title}}{The title}
+
+\item{\code{ds}}{A list of mkinds objects}
+
+\item{\code{f_time_norm}}{Time normalisation factors}
+
+\item{\code{meta}}{The meta data}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{mkindsg$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
diff --git a/man/print.mkinds.Rd b/man/print.mkinds.Rd
deleted file mode 100644
index 51ef3b76..00000000
--- a/man/print.mkinds.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mkinds.R
-\name{print.mkinds}
-\alias{print.mkinds}
-\title{Print mkinds objects}
-\usage{
-\method{print}{mkinds}(x, ...)
-}
-\arguments{
-\item{x}{An \code{\link{mkinds}} object.}
-
-\item{\dots}{Not used.}
-}
-\description{
-Print mkinds objects
-}