Temporarily remove @example tags

Due to r-lib/roxygen2#1158

5 files changed, 398 insertions, 43 deletions

diff --git a/man/chent.Rd b/man/chent.Rd
index 29fba70..a1a5fe8 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -1,20 +1,19 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/chent.R
-\docType{class}
 \name{chent}
 \alias{chent}
 \title{An R6 class for chemical entities with associated data}
-\format{An \code{\link{R6Class}} generator object}
-\usage{
-chent
+\format{
+An \code{\link{R6Class}} generator object
 }
 \description{
 The class is initialised with an identifier. Chemical information is retrieved from
 the internet. Additionally, it can be generated using RDKit if RDKit and its
 python bindings are installed and configured for use with PythonInR.
 }
-\section{Fields}{
-
+\keyword{data}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
 \describe{
 \item{\code{identifier}}{The identifier that was used to initiate the object, with attribute 'source'}
 
@@ -50,18 +49,258 @@ configured for use with PythonInR}
 \item{\code{soil_sorption}}{Dataframe of soil sorption data}
 
 \item{\code{PUF}}{Plant uptake factor}
-}}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{chent$new()}}
+\item \href{#method-try_pubchem}{\code{chent$try_pubchem()}}
+\item \href{#method-get_pubchem}{\code{chent$get_pubchem()}}
+\item \href{#method-get_rdkit}{\code{chent$get_rdkit()}}
+\item \href{#method-get_chyaml}{\code{chent$get_chyaml()}}
+\item \href{#method-add_p0}{\code{chent$add_p0()}}
+\item \href{#method-add_cwsat}{\code{chent$add_cwsat()}}
+\item \href{#method-add_PUF}{\code{chent$add_PUF()}}
+\item \href{#method-add_TP}{\code{chent$add_TP()}}
+\item \href{#method-add_transformation}{\code{chent$add_transformation()}}
+\item \href{#method-add_soil_degradation}{\code{chent$add_soil_degradation()}}
+\item \href{#method-add_soil_ff}{\code{chent$add_soil_ff()}}
+\item \href{#method-add_soil_sorption}{\code{chent$add_soil_sorption()}}
+\item \href{#method-pdf}{\code{chent$pdf()}}
+\item \href{#method-png}{\code{chent$png()}}
+\item \href{#method-emf}{\code{chent$emf()}}
+\item \href{#method-clone}{\code{chent$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$new(
+  identifier,
+  smiles = NULL,
+  smiles_source = "user",
+  inchikey = NULL,
+  inchikey_source = "user",
+  pubchem = TRUE,
+  pubchem_from = c("name", "smiles", "inchikey"),
+  rdkit = TRUE,
+  template = NULL,
+  chyaml = TRUE
+)}\if{html}{\out{</div>}}
+}
 
-\examples{
-oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
-print(oct)
-if (!is.null(oct$Picture)) {
-  plot(oct)
 }
-caffeine <- chent$new("caffeine")
-print(caffeine)
-if (!is.null(caffeine$Picture)) {
-  plot(caffeine)
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-try_pubchem"></a>}}
+\if{latex}{\out{\hypertarget{method-try_pubchem}{}}}
+\subsection{Method \code{try_pubchem()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_pubchem"></a>}}
+\if{latex}{\out{\hypertarget{method-get_pubchem}{}}}
+\subsection{Method \code{get_pubchem()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_rdkit"></a>}}
+\if{latex}{\out{\hypertarget{method-get_rdkit}{}}}
+\subsection{Method \code{get_rdkit()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_chyaml"></a>}}
+\if{latex}{\out{\hypertarget{method-get_chyaml}{}}}
+\subsection{Method \code{get_chyaml()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$get_chyaml(
+  repo = c("wd", "local", "web"),
+  chyaml = paste0(URLencode(self$identifier), ".yaml")
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_p0"></a>}}
+\if{latex}{\out{\hypertarget{method-add_p0}{}}}
+\subsection{Method \code{add_p0()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_cwsat"></a>}}
+\if{latex}{\out{\hypertarget{method-add_cwsat}{}}}
+\subsection{Method \code{add_cwsat()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_PUF"></a>}}
+\if{latex}{\out{\hypertarget{method-add_PUF}{}}}
+\subsection{Method \code{add_PUF()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF(
+  PUF = 0,
+  source = "focus_generic_gw_2014",
+  page = 41,
+  remark = "Conservative default value"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_TP"></a>}}
+\if{latex}{\out{\hypertarget{method-add_TP}{}}}
+\subsection{Method \code{add_TP()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_transformation"></a>}}
+\if{latex}{\out{\hypertarget{method-add_transformation}{}}}
+\subsection{Method \code{add_transformation()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_transformation(
+  study_type,
+  TP_identifier,
+  max_occurrence,
+  remark = "",
+  source = NA,
+  pages = NA
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_soil_degradation"></a>}}
+\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}}
+\subsection{Method \code{add_soil_degradation()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_degradation(
+  soils,
+  DT50_mod,
+  DT50_mod_ref,
+  type = NA,
+  country = NA,
+  pH_orig = NA,
+  pH_medium = NA,
+  pH_H2O = NA,
+  perc_OC = NA,
+  temperature = NA,
+  moisture = NA,
+  category = "lab",
+  formulation = NA,
+  model = NA,
+  chi2 = NA,
+  remark = "",
+  source,
+  page = NA
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_soil_ff"></a>}}
+\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}}
+\subsection{Method \code{add_soil_ff()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_soil_sorption"></a>}}
+\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}}
+\subsection{Method \code{add_soil_sorption()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_sorption(
+  soils,
+  Kf,
+  Kfoc,
+  N,
+  type = NA,
+  pH_orig = NA,
+  pH_medium = NA,
+  pH_H2O = NA,
+  perc_OC = NA,
+  perc_clay = NA,
+  CEC = NA,
+  remark = "",
+  source,
+  page = NA
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-pdf"></a>}}
+\if{latex}{\out{\hypertarget{method-pdf}{}}}
+\subsection{Method \code{pdf()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$pdf(
+  file = paste0(self$identifier, ".pdf"),
+  dir = "structures/pdf",
+  template = NULL
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-png"></a>}}
+\if{latex}{\out{\hypertarget{method-png}{}}}
+\subsection{Method \code{png()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$png(
+  file = paste0(self$identifier, ".png"),
+  dir = "structures/png",
+  antialias = "gray"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-emf"></a>}}
+\if{latex}{\out{\hypertarget{method-emf}{}}}
+\subsection{Method \code{emf()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$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>}}
+}
 }
 }
-\keyword{data}
diff --git a/man/draw_svg.chent.Rd b/man/draw_svg.chent.Rd
index 93b657d..2125b47 100644
--- a/man/draw_svg.chent.Rd
+++ b/man/draw_svg.chent.Rd
@@ -4,8 +4,13 @@
 \alias{draw_svg.chent}
 \title{Draw SVG graph from a chent object using RDKit}
 \usage{
-draw_svg.chent(x, width = 300, height = 150,
-  filename = paste0(names(x$identifier), ".svg"), subdir = "svg")
+draw_svg.chent(
+  x,
+  width = 300,
+  height = 150,
+  filename = paste0(names(x$identifier), ".svg"),
+  subdir = "svg"
+)
 }
 \arguments{
 \item{x}{The chent object to be plotted}
diff --git a/man/pai.Rd b/man/pai.Rd
index 96f21d0..6a243ab 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -4,24 +4,91 @@
 \name{pai}
 \alias{pai}
 \title{An R6 class for pesticidal active ingredients and associated data}
-\format{An \code{\link{R6Class}} generator object}
-\usage{
-pai
+\format{
+An \code{\link{R6Class}} generator object
 }
 \description{
 The class is initialised with an identifier which is generally an ISO common name.
 Additional chemical information is retrieved from the internet if available.
 }
-\section{Fields}{
-
+\keyword{data}
+\section{Super class}{
+\code{\link[chents:chent]{chents::chent}} -> \code{pai}
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
 \describe{
 \item{\code{iso}}{ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides}
 
 \item{\code{alanwood}}{List of information retreived from www.alanwood.net/pesticides}
-}}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{pai$new()}}
+\item \href{#method-clone}{\code{pai$clone()}}
+}
+}
+\if{html}{
+\out{<details ><summary>Inherited methods</summary>}
+\itemize{
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF">}\href{../../chents/html/chent.html#method-add_PUF}{\code{chents::chent$add_PUF()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP">}\href{../../chents/html/chent.html#method-add_TP}{\code{chents::chent$add_TP()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat">}\href{../../chents/html/chent.html#method-add_cwsat}{\code{chents::chent$add_cwsat()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0">}\href{../../chents/html/chent.html#method-add_p0}{\code{chents::chent$add_p0()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation">}\href{../../chents/html/chent.html#method-add_soil_degradation}{\code{chents::chent$add_soil_degradation()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff">}\href{../../chents/html/chent.html#method-add_soil_ff}{\code{chents::chent$add_soil_ff()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption">}\href{../../chents/html/chent.html#method-add_soil_sorption}{\code{chents::chent$add_soil_sorption()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation">}\href{../../chents/html/chent.html#method-add_transformation}{\code{chents::chent$add_transformation()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf">}\href{../../chents/html/chent.html#method-emf}{\code{chents::chent$emf()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml">}\href{../../chents/html/chent.html#method-get_chyaml}{\code{chents::chent$get_chyaml()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem">}\href{../../chents/html/chent.html#method-get_pubchem}{\code{chents::chent$get_pubchem()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit">}\href{../../chents/html/chent.html#method-get_rdkit}{\code{chents::chent$get_rdkit()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf">}\href{../../chents/html/chent.html#method-pdf}{\code{chents::chent$pdf()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png">}\href{../../chents/html/chent.html#method-png}{\code{chents::chent$png()}}\out{</span>}
+\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem">}\href{../../chents/html/chent.html#method-try_pubchem}{\code{chents::chent$try_pubchem()}}\out{</span>}
+}
+\out{</details>}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{pai$new(
+  iso,
+  identifier = iso,
+  smiles = NULL,
+  smiles_source = "user",
+  inchikey = NULL,
+  inchikey_source = "user",
+  alanwood = TRUE,
+  pubchem = TRUE,
+  pubchem_from = "auto",
+  rdkit = TRUE,
+  template = NULL,
+  chyaml = TRUE
+)}\if{html}{\out{</div>}}
+}
 
-\examples{
-atr <- pai$new("atrazine")
-print(atr)
 }
-\keyword{data}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{pai$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/plot.chent.Rd b/man/plot.chent.Rd
index f2850fa..e5a8770 100644
--- a/man/plot.chent.Rd
+++ b/man/plot.chent.Rd
@@ -14,10 +14,3 @@
 \description{
 Plot method for chent objects
 }
-\examples{
-caffeine <- chent$new("caffeine")
-print(caffeine)
-if (!is.null(caffeine$Picture)) {
-  plot(caffeine)
-}
-}
diff --git a/man/pp.Rd b/man/pp.Rd
index 3957de7..cd950df 100644
--- a/man/pp.Rd
+++ b/man/pp.Rd
@@ -4,15 +4,15 @@
 \name{pp}
 \alias{pp}
 \title{R6 class for holding a product with at least one active ingredient}
-\format{An \code{\link{R6Class}} generator object.}
-\usage{
-pp
+\format{
+An \code{\link{R6Class}} generator object.
 }
 \description{
 An R6 class for holding information about a product with at least one active ingredient
 }
-\section{Fields}{
-
+\keyword{data}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
 \describe{
 \item{\code{name}}{The name of the product}
 
@@ -21,6 +21,57 @@ An R6 class for holding information about a product with at least one active ing
 \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-new}{\code{pp$new()}}
+\item \href{#method-print}{\code{pp$print()}}
+\item \href{#method-clone}{\code{pp$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{pp$new(
+  name,
+  ...,
+  concentrations,
+  concentration_units = "g/L",
+  density = 1000,
+  density_units = "g/L"
+)}\if{html}{\out{</div>}}
+}
 
-\keyword{data}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-print"></a>}}
+\if{latex}{\out{\hypertarget{method-print}{}}}
+\subsection{Method \code{print()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{pp$print()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{pp$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>}}
+}
+}
+}