Temporarily remove @example tags

Due to r-lib/roxygen2#1158

1 files changed, 256 insertions, 17 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}