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()

1 files changed, 100 insertions, 0 deletions

diff --git a/man/mkindsg.Rd b/man/mkindsg.Rd
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+++ b/man/mkindsg.Rd
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+% 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>}}
+}
+}
+}