Start new version, rename pp to ppp, more docs

4 files changed, 265 insertions, 82 deletions

diff --git a/man/chent.Rd b/man/chent.Rd
index e069938..686d6c7 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -73,7 +73,8 @@ Add a line in the internal dataframe holding modelling DT50 values}
 
 \item{\code{soil_ff}}{Dataframe of formation fractions}
 
-\item{\code{soil_sorption}}{Dataframe of soil sorption data}
+\item{\code{soil_sorption}}{Dataframe of soil sorption data
+Add soil sorption data}
 }
 \if{html}{\out{</div>}}
 }
@@ -214,7 +215,9 @@ Obtain information from a YAML file}
 \describe{
 \item{\code{repo}}{Should the file be looked for in the current working
 directory, a local git repository under \verb{~/git/chyaml}, or from
-the web (not implemented).
+the web (not implemented).}
+
+\item{\code{chyaml}}{The filename to be looked for
 Add a vapour pressure}
 }
 \if{html}{\out{</div>}}
@@ -256,7 +259,17 @@ Add a water solubility}
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
-\item{\code{p0}}{The water solubility in mg/L
+\item{\code{cwsat}}{The water solubility in mg/L}
+
+\item{\code{T}}{Temperature}
+
+\item{\code{pH}}{The pH value}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+
+\item{\code{remark}}{A remark
 Add a plant uptake factor}
 }
 \if{html}{\out{</div>}}
@@ -279,6 +292,12 @@ Add a plant uptake factor}
 \if{html}{\out{<div class="arguments">}}
 \describe{
 \item{\code{PUF}}{The plant uptake factor, a number between 0 and 1}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+
+\item{\code{remark}}{A remark}
 }
 \if{html}{\out{</div>}}
 }
@@ -318,6 +337,26 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{study_type}}{A characterisation of the study type}
+
+\item{\code{TP_identifier}}{An identifier of one of the transformation products
+in \code{self$TPs}}
+
+\item{\code{max_occurrence}}{The maximum observed occurrence of the
+transformation product, expressed as a fraction of the amount that would
+result from stochiometric transformation}
+
+\item{\code{remark}}{A remark}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{pages}}{The page from which the information was taken}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_soil_degradation"></a>}}
@@ -346,6 +385,50 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{soils}}{Names of the soils}
+
+\item{\code{DT50_mod}}{The modelling DT50 in the sense of regulatory pesticide
+fate modelling}
+
+\item{\code{DT50_mod_ref}}{The normalised modelling DT50 in the sense of
+regulatory pesticide fate modelling}
+
+\item{\code{type}}{The soil type}
+
+\item{\code{country}}{The country (mainly for field studies)}
+
+\item{\code{pH_orig}}{The pH stated in the study}
+
+\item{\code{pH_medium}}{The medium in which this pH was measured}
+
+\item{\code{pH_H2O}}{The pH extrapolated to pure water}
+
+\item{\code{perc_OC}}{The percentage of organic carbon in the soil}
+
+\item{\code{temperature}}{The temperature during the study in degrees Celsius}
+
+\item{\code{moisture}}{The moisture during the study}
+
+\item{\code{category}}{Is it a laboratory ('lab') or field study ('field')}
+
+\item{\code{formulation}}{Name of the formulation applied, if it was not
+the technical active ingredient}
+
+\item{\code{model}}{The degradation model used for deriving \code{DT50_mod}}
+
+\item{\code{chi2}}{The relative error as defined in FOCUS kinetics}
+
+\item{\code{remark}}{A remark}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_soil_ff"></a>}}
@@ -355,6 +438,17 @@ Add a plant uptake factor}
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{target}}{The identifier(s) of the transformation product}
+
+\item{\code{soils}}{The soil name(s) in which the transformation was observed}
+
+\item{\code{ff}}{The formation fraction(s)}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}}
@@ -379,6 +473,23 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{Kf}}{The sorption constant in L/kg, either linear (then \code{N} is 1)
+or according to Freundlich}
+
+\item{\code{Kfoc}}{The constant from above, normalised to soil organic carbon}
+
+\item{\code{N}}{The Freundlich exponent}
+
+\item{\code{perc_clay}}{The percentage of clay in the soil}
+
+\item{\code{CEC}}{The cation exchange capacity
+Write a PDF image of the structure}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-pdf"></a>}}
@@ -392,6 +503,18 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{file}}{The file to write to}
+
+\item{\code{dir}}{The directory to write the file to}
+
+\item{\code{template}}{A template expressed as SMILES to use in RDKit
+Write a PNG image of the structure}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-png"></a>}}
@@ -405,6 +528,14 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{antialias}}{Passed to \link[grDevices:png]{png}
+Write an EMF image of the structure using \link[devEMF:emf]{emf}}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-emf"></a>}}
@@ -414,6 +545,13 @@ Add a plant uptake factor}
 \if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{file}}{The file to write to}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-clone"></a>}}
diff --git a/man/pai.Rd b/man/pai.Rd
index d966a9e..f133c5a 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -8,6 +8,11 @@
 An \code{\link{R6Class}} generator object
 }
 \description{
+An R6 class for pesticidal active ingredients and associated data
+
+An R6 class for pesticidal active ingredients and associated data
+}
+\details{
 The class is initialised with an identifier which is generally an ISO common name.
 Additional chemical information is retrieved from the internet if available.
 }
@@ -31,9 +36,11 @@ if (!is.null(atr$Picture)) {
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
 \describe{
-\item{\code{iso}}{ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org}
+\item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750}
 
-\item{\code{bcpc}}{List of information retrieved from pesticidecompendium.bcpc.org}
+\item{\code{bcpc}}{Information retrieved from the BCPC compendium available online
+at <pesticidecompendium.bcpc.org>
+Creates a new instance of this \link[R6:R6Class]{R6} class.}
 }
 \if{html}{\out{</div>}}
 }
@@ -69,6 +76,11 @@ if (!is.null(atr$Picture)) {
 \if{html}{\out{<a id="method-pai-new"></a>}}
 \if{latex}{\out{\hypertarget{method-pai-new}{}}}
 \subsection{Method \code{new()}}{
+This class is derived from \link{chent}. It makes it easy
+to create a \link{chent} from the ISO common name of a pesticide active
+ingredient, and additionally stores the ISO name as well as
+the complete result of querying the BCPC compendium using
+\link[webchem:bcpc_query]{bcpc_query}.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{pai$new(
   iso,
@@ -84,6 +96,16 @@ if (!is.null(atr$Picture)) {
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{iso}}{The ISO common name to be used in the query of the
+BCPC compendium}
+
+\item{\code{identifier}}{Alternative identifier used for querying pubchem}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-pai-clone"></a>}}
diff --git a/man/pp.Rd b/man/pp.Rd
deleted file mode 100644
index 363f9ba..0000000
--- a/man/pp.Rd
+++ /dev/null
@@ -1,77 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/chent.R
-\docType{class}
-\name{pp}
-\alias{pp}
-\title{R6 class for holding a product with at least one active ingredient}
-\format{
-An \code{\link{R6Class}} generator object.
-}
-\description{
-An R6 class for holding information about a product with at least one active ingredient
-}
-\keyword{data}
-\section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{name}}{The name of the product}
-
-\item{\code{ais}}{A list of active ingredients}
-
-\item{\code{concentrations}}{The concentration of the ais}
-
-\item{\code{concentration_units}}{Defaults to g/L}
-}
-\if{html}{\out{</div>}}
-}
-\section{Methods}{
-\subsection{Public methods}{
-\itemize{
-\item \href{#method-pp-new}{\code{pp$new()}}
-\item \href{#method-pp-print}{\code{pp$print()}}
-\item \href{#method-pp-clone}{\code{pp$clone()}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pp-new"></a>}}
-\if{latex}{\out{\hypertarget{method-pp-new}{}}}
-\subsection{Method \code{new()}}{
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{pp$new(
-  name,
-  ...,
-  concentrations,
-  concentration_units = "g/L",
-  density = 1000,
-  density_units = "g/L"
-)}\if{html}{\out{</div>}}
-}
-
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pp-print"></a>}}
-\if{latex}{\out{\hypertarget{method-pp-print}{}}}
-\subsection{Method \code{print()}}{
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{pp$print()}\if{html}{\out{</div>}}
-}
-
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pp-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-pp-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{pp$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/ppp.Rd b/man/ppp.Rd
new file mode 100644
index 0000000..c0d35f1
--- /dev/null
+++ b/man/ppp.Rd
@@ -0,0 +1,100 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/chent.R
+\docType{class}
+\name{ppp}
+\alias{ppp}
+\title{R6 class for a plant protection product with at least one active ingredient}
+\format{
+An \code{\link{R6Class}} generator object.
+}
+\description{
+Contains basic information about the active ingredients in the
+product
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{name}}{The name of the product}
+
+\item{\code{ais}}{A list of active ingredients}
+
+\item{\code{concentrations}}{The concentration of the ais}
+
+\item{\code{concentration_units}}{Defaults to g/L}
+
+\item{\code{density}}{The density of the product}
+
+\item{\code{density_units}}{Defaults to g/L
+Creates a new instance of this \link[R6:R6Class]{R6} class.}
+
+\item{\code{...}}{Identifiers of the active ingredients}
+
+\item{\code{concentrations}}{Concentrations of the active ingredients}
+
+\item{\code{concentration_units}}{Defaults to g/L}
+
+\item{\code{density}}{The density}
+
+\item{\code{density_units}}{Defaults to g/L
+Printing method}
+}
+\if{html}{\out{</div>}}
+}
+\section{Active bindings}{
+\if{html}{\out{<div class="r6-active-bindings">}}
+\describe{
+\item{\code{...}}{Identifiers of the active ingredients}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-ppp-new}{\code{ppp$new()}}
+\item \href{#method-ppp-print}{\code{ppp$print()}}
+\item \href{#method-ppp-clone}{\code{ppp$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ppp-new"></a>}}
+\if{latex}{\out{\hypertarget{method-ppp-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ppp$new(
+  name,
+  ...,
+  concentrations,
+  concentration_units = "g/L",
+  density = 1000,
+  density_units = "g/L"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ppp-print"></a>}}
+\if{latex}{\out{\hypertarget{method-ppp-print}{}}}
+\subsection{Method \code{print()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ppp$print()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ppp-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-ppp-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ppp$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>}}
+}
+}
+}