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| -rw-r--r-- | man/pai.Rd | 163 | ||||
| -rw-r--r-- | man/plot.chent.Rd | 12 | ||||
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| -rw-r--r-- | man/ppp.Rd | 87 | ||||
| -rw-r--r-- | man/print.ppp.Rd | 16 |
12 files changed, 644 insertions, 308 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index a1a5fe8..ca5f267 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -4,198 +4,357 @@ \alias{chent} \title{An R6 class for chemical entities with associated data} \format{ -An \code{\link{R6Class}} generator object +An \link[R6:R6Class]{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. +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. +} +\examples{ +# Don't run examples per default, as PubChem may be unavailable +\dontrun{ +caffeine <- chent$new("caffeine") +print(caffeine) +if (!is.null(caffeine$Picture)) { + plot(caffeine) +} +oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) +print(oct) +} } -\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'} + \if{html}{\out{<div class="r6-fields">}} + \describe{ + \item{\code{identifier}}{(\code{character(1)})\cr +The identifier that was used to initiate the object, with attribute 'source'} -\item{\code{inchikey}}{InChI Key, with attribute 'source'} + \item{\code{inchikey}}{(\code{character(1)})\cr +InChI Key, with attribute 'source'} -\item{\code{smiles}}{SMILES code, with attribute 'source'} + \item{\code{smiles}}{(\code{character()})\cr +SMILES code(s), with attribute 'source'} -\item{\code{mw}}{Molecular weight, with attribute 'source'} + \item{\code{mw}}{(\code{numeric(1)})\cr +Molecular weight, with attribute 'source'} -\item{\code{pubchem}}{List of information retreived from PubChem} + \item{\code{pubchem}}{(\code{list()})\cr +List of information retrieved from PubChem} -\item{\code{rdkit}}{List of information obtained with RDKit, if installed and -configured for use with PythonInR} + \item{\code{rdkit}}{List of information obtained with RDKit} -\item{\code{svg}}{SVG code} + \item{\code{mol}}{<rdkit.Chem.rdchem.Mol> object} -\item{\code{Picture}}{Graph as a \code{\link{picture}} object obtained using grImport} + \item{\code{svg}}{SVG code} -\item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file} + \item{\code{Picture}}{Graph as a \link[grImport:Picture-class]{grImport::Picture} object obtained using the grImport package} -\item{\code{pdf_height}}{Height of the MediaBox in the pdf after cropping} + \item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file} -\item{\code{p0}}{Vapour pressure in Pa} + \item{\code{pdf_height}}{Height of the MediaBox in the pdf after cropping} -\item{\code{cwsat}}{Water solubility in mg/L} + \item{\code{p0}}{Vapour pressure in Pa} -\item{\code{chyaml}}{List of information obtained from a YAML file} + \item{\code{cwsat}}{Water solubility in mg/L} -\item{\code{soil_degradation}}{Dataframe of modelling DT50 values} + \item{\code{PUF}}{Plant uptake factor} -\item{\code{soil_ff}}{Dataframe of formation fractions} + \item{\code{chyaml}}{List of information obtained from a YAML file} -\item{\code{soil_sorption}}{Dataframe of soil sorption data} + \item{\code{TPs}}{List of transformation products as chent objects} -\item{\code{PUF}}{Plant uptake factor} -} -\if{html}{\out{</div>}} + \item{\code{transformations}}{Data frame of observed transformations} + + \item{\code{soil_degradation}}{Dataframe of modelling DT50 values} + + \item{\code{soil_ff}}{Dataframe of formation fractions} + + \item{\code{soil_sorption}}{Dataframe of soil sorption data} + } + \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()}} -} + \itemize{ + \item \href{#method-chent-initialize}{\code{chent$new()}} + \item \href{#method-chent-try_pubchem}{\code{chent$try_pubchem()}} + \item \href{#method-chent-get_pubchem}{\code{chent$get_pubchem()}} + \item \href{#method-chent-get_rdkit}{\code{chent$get_rdkit()}} + \item \href{#method-chent-get_chyaml}{\code{chent$get_chyaml()}} + \item \href{#method-chent-add_p0}{\code{chent$add_p0()}} + \item \href{#method-chent-add_cwsat}{\code{chent$add_cwsat()}} + \item \href{#method-chent-add_PUF}{\code{chent$add_PUF()}} + \item \href{#method-chent-add_TP}{\code{chent$add_TP()}} + \item \href{#method-chent-add_transformation}{\code{chent$add_transformation()}} + \item \href{#method-chent-add_soil_degradation}{\code{chent$add_soil_degradation()}} + \item \href{#method-chent-add_soil_ff}{\code{chent$add_soil_ff()}} + \item \href{#method-chent-add_soil_sorption}{\code{chent$add_soil_sorption()}} + \item \href{#method-chent-pdf}{\code{chent$pdf()}} + \item \href{#method-chent-png}{\code{chent$png()}} + \item \href{#method-chent-emf}{\code{chent$emf()}} + \item \href{#method-chent-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( +\if{html}{\out{<a id="method-chent-initialize"></a>}} +\if{latex}{\out{\hypertarget{method-chent-initialize}{}}} +\subsection{\code{chent$new()}}{ + Creates a new instance of this \link[R6:R6Class]{R6} class. + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$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>}} + chyaml = FALSE +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{identifier}}{Identifier to be stored in the object} + \item{\code{smiles}}{Optional user provided SMILES code} + \item{\code{inchikey}}{Optional user provided InChI Key} + \item{\code{pubchem}}{Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?} + \item{\code{pubchem_from}}{Possibility to select the argument +that is used to query pubchem} + \item{\code{rdkit}}{Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?} + \item{\code{template}}{An optional SMILES code to be used as template for RDKit} + \item{\code{chyaml}}{Should we look for a identifier.yaml file in the working +directory?} + } + \if{html}{\out{</div>}} + } } -} \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$try_pubchem(query, from = "name")}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-try_pubchem"></a>}} +\if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} +\subsection{\code{chent$try_pubchem()}}{ + Try to get chemical information from PubChem + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$try_pubchem(query = self$identifier, from = "name")} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{query}}{Query string to be passed to \link[webchem:get_cid]{get_cid}} + \item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid}} + } + \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$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-get_pubchem"></a>}} +\if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}} +\subsection{\code{chent$get_pubchem()}}{ + Get chemical information from PubChem for a known PubChem CID + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$get_pubchem(pubchem_cid)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{pubchem_cid}}{CID} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-get_rdkit"></a>}} -\if{latex}{\out{\hypertarget{method-get_rdkit}{}}} -\subsection{Method \code{get_rdkit()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-get_rdkit"></a>}} +\if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} +\subsection{\code{chent$get_rdkit()}}{ + Get chemical information from RDKit if available + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$get_rdkit(template = NULL)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{template}}{An optional SMILES code to be used as template for RDKit} + } + \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$get_chyaml( +\if{html}{\out{<a id="method-chent-get_chyaml"></a>}} +\if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}} +\subsection{\code{chent$get_chyaml()}}{ + Obtain information from a YAML file + \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{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \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).} + \item{\code{chyaml}}{The filename to be looked for} + } + \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$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-add_p0"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} +\subsection{\code{chent$add_p0()}}{ + Add a vapour pressure + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{p0}}{The vapour pressure in Pa} + \item{\code{T}}{Temperature} + \item{\code{source}}{An acronym specifying the source of the information} + \item{\code{page}}{The page from which the information was taken} + \item{\code{remark}}{A remark} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_cwsat"></a>}} -\if{latex}{\out{\hypertarget{method-add_cwsat}{}}} -\subsection{Method \code{add_cwsat()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-add_cwsat"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}} +\subsection{\code{chent$add_cwsat()}}{ + Add a water solubility + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{cwsat}}{The water solubility in mg/L} + \item{\code{T}}{Temperature} + \item{\code{pH}}{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} + } + \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$add_PUF( +\if{html}{\out{<a id="method-chent-add_PUF"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} +\subsection{\code{chent$add_PUF()}}{ + Add a plant uptake factor + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_PUF( PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value" -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{PUF}}{The plant uptake factor, a number between 0 and 1} + \item{\code{source}}{An acronym specifying the source of the information} + \item{\code{page}}{The page from which the information was taken} + \item{\code{remark}}{A remark} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_TP"></a>}} -\if{latex}{\out{\hypertarget{method-add_TP}{}}} -\subsection{Method \code{add_TP()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-add_TP"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_TP}{}}} +\subsection{\code{chent$add_TP()}}{ + Add a transformation product to the internal list + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object} + \item{\code{smiles}}{Optional user provided SMILES code} + \item{\code{pubchem}}{Should chemical information be obtained from PubChem?} + } + \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$add_transformation( +\if{html}{\out{<a id="method-chent-add_transformation"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} +\subsection{\code{chent$add_transformation()}}{ + Add a line in the internal dataframe holding observed transformations + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = "", source = NA, pages = NA -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{study_type}}{A characterisation of the study type} + \item{\code{TP_identifier}}{An identifier of one of the transformation products +in \code{self$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 pages from which the information was taken} + } + \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$add_soil_degradation( +\if{html}{\out{<a id="method-chent-add_soil_degradation"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}} +\subsection{\code{chent$add_soil_degradation()}}{ + Add a line in the internal dataframe holding modelling DT50 values + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_soil_degradation( soils, DT50_mod, DT50_mod_ref, @@ -214,25 +373,70 @@ configured for use with PythonInR} remark = "", source, page = NA -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{soils}}{Names of the soils} + \item{\code{DT50_mod}}{The modelling DT50 in the sense of regulatory pesticide +fate modelling} + \item{\code{DT50_mod_ref}}{The normalised modelling DT50 in the sense of +regulatory pesticide fate modelling} + \item{\code{type}}{The soil type} + \item{\code{country}}{The country (mainly for field studies)} + \item{\code{pH_orig}}{The pH stated in the study} + \item{\code{pH_medium}}{The medium in which this pH was measured} + \item{\code{pH_H2O}}{The pH extrapolated to pure water} + \item{\code{perc_OC}}{The percentage of organic carbon in the soil} + \item{\code{temperature}}{The temperature during the study in degrees Celsius} + \item{\code{moisture}}{The moisture during the study} + \item{\code{category}}{Is it a laboratory ('lab') or field study ('field')} + \item{\code{formulation}}{Name of the formulation applied, if it was not +the technical active ingredient} + \item{\code{model}}{The degradation model used for deriving \code{DT50_mod}} + \item{\code{chi2}}{The relative error as defined in FOCUS kinetics} + \item{\code{remark}}{A remark} + \item{\code{source}}{An acronym specifying the source of the information} + \item{\code{page}}{The page from which the information was taken} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_soil_ff"></a>}} -\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}} -\subsection{Method \code{add_soil_ff()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-add_soil_ff"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} +\subsection{\code{chent$add_soil_ff()}}{ + Add one or more formation fractions for degradation in soil + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)} + \if{html}{\out{</div>}} + } + \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)} + \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-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$add_soil_sorption( +\if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}} +\subsection{\code{chent$add_soil_sorption()}}{ + Add soil sorption data + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_soil_sorption( soils, Kf, Kfoc, @@ -247,60 +451,119 @@ configured for use with PythonInR} remark = "", source, page = NA -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{soils}}{Names of the soils} + \item{\code{Kf}}{The sorption constant in L/kg, either linear (then \code{N} is 1) +or according to Freundlich} + \item{\code{Kfoc}}{The constant from above, normalised to soil organic carbon} + \item{\code{N}}{The Freundlich exponent} + \item{\code{type}}{The soil type} + \item{\code{pH_orig}}{The pH stated in the study} + \item{\code{pH_medium}}{The medium in which this pH was measured} + \item{\code{pH_H2O}}{The pH extrapolated to pure water} + \item{\code{perc_OC}}{The percentage of organic carbon in the soil} + \item{\code{perc_clay}}{The percentage of clay in the soil} + \item{\code{CEC}}{The cation exchange capacity} + \item{\code{remark}}{A remark} + \item{\code{source}}{An acronym specifying the source of the information} + \item{\code{page}}{The page from which the information was taken} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-pdf"></a>}} -\if{latex}{\out{\hypertarget{method-pdf}{}}} -\subsection{Method \code{pdf()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$pdf( +\if{html}{\out{<a id="method-chent-pdf"></a>}} +\if{latex}{\out{\hypertarget{method-chent-pdf}{}}} +\subsection{\code{chent$pdf()}}{ + Write a PDF image of the structure + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$pdf( file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", template = NULL -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{file}}{The file to write to} + \item{\code{dir}}{The directory to write the file to} + \item{\code{template}}{An optional SMILES code to be used as template for RDKit} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-png"></a>}} -\if{latex}{\out{\hypertarget{method-png}{}}} -\subsection{Method \code{png()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$png( +\if{html}{\out{<a id="method-chent-png"></a>}} +\if{latex}{\out{\hypertarget{method-chent-png}{}}} +\subsection{\code{chent$png()}}{ + Write a PNG image of the structure + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$png( file = paste0(self$identifier, ".png"), dir = "structures/png", antialias = "gray" -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{file}}{The file to write to} + \item{\code{dir}}{The directory to write the file to} + \item{\code{antialias}}{Passed to \link[grDevices:png]{png}} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-emf"></a>}} -\if{latex}{\out{\hypertarget{method-emf}{}}} -\subsection{Method \code{emf()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-emf"></a>}} +\if{latex}{\out{\hypertarget{method-chent-emf}{}}} +\subsection{\code{chent$emf()}}{ + Write an EMF image of the structure using \link[devEMF:emf]{emf} + \subsection{Usage}{ + \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} + \item{\code{dir}}{The directory to write the file to} + } + \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$clone(deep = FALSE)}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-chent-clone"></a>}} +\if{latex}{\out{\hypertarget{method-chent-clone}{}}} +\subsection{\code{chent$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>}} + } } -\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/figures/README-caffeine-1.png b/man/figures/README-caffeine-1.png Binary files differnew file mode 100644 index 0000000..aadb576 --- /dev/null +++ b/man/figures/README-caffeine-1.png diff --git a/man/figures/README-plot-caffeine-1.png b/man/figures/README-plot-caffeine-1.png Binary files differnew file mode 100644 index 0000000..21caae7 --- /dev/null +++ b/man/figures/README-plot-caffeine-1.png diff --git a/man/figures/README-unnamed-chunk-3-1.png b/man/figures/README-unnamed-chunk-3-1.png Binary files differnew file mode 100644 index 0000000..9646595 --- /dev/null +++ b/man/figures/README-unnamed-chunk-3-1.png diff --git a/man/figures/README-unnamed-chunk-4-1.png b/man/figures/README-unnamed-chunk-4-1.png Binary files differnew file mode 100644 index 0000000..7e7352d --- /dev/null +++ b/man/figures/README-unnamed-chunk-4-1.png diff --git a/man/figures/README-unnamed-chunk-5-1.png b/man/figures/README-unnamed-chunk-5-1.png Binary files differnew file mode 100644 index 0000000..7e7352d --- /dev/null +++ b/man/figures/README-unnamed-chunk-5-1.png diff --git a/man/figures/README-unnamed-chunk-6-1.png b/man/figures/README-unnamed-chunk-6-1.png Binary files differnew file mode 100644 index 0000000..bf6cdb4 --- /dev/null +++ b/man/figures/README-unnamed-chunk-6-1.png @@ -1,94 +1,131 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/chent.R -\docType{class} \name{pai} \alias{pai} \title{An R6 class for pesticidal active ingredients and associated data} \format{ -An \code{\link{R6Class}} generator object +An \link[R6:R6Class]{R6::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. +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}. +} +\examples{ +# Don't run examples per default, as PubChem may be unavailable +\dontrun{ +atr <- pai$new("atrazine") +print(atr) +if (!is.null(atr$Picture)) { + plot(atr) +} +# We can also define pais that are not found on the BCPC site +decanol <- pai$new("1-Decanol") +print(decanol) +} } -\keyword{data} \section{Super class}{ -\code{\link[chents:chent]{chents::chent}} -> \code{pai} +\code{\link[chents:chent]{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} + \if{html}{\out{<div class="r6-fields">}} + \describe{ + \item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750} -\item{\code{alanwood}}{List of information retreived from www.alanwood.net/pesticides} -} -\if{html}{\out{</div>}} + \item{\code{bcpc}}{Information retrieved from the BCPC compendium available online +at <pesticidecompendium.bcpc.org>} + } + \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$try_pubchem()}}\out{</span>} -} -\out{</details>} -} + \itemize{ + \item \href{#method-pai-initialize}{\code{pai$new()}} + \item \href{#method-pai-clone}{\code{pai$clone()}} + } +} +\if{html}{\out{<details><summary>Inherited methods</summary> +<ul> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-chent-add_PUF'><code>chent$add_PUF()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-chent-add_TP'><code>chent$add_TP()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-chent-add_cwsat'><code>chent$add_cwsat()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-chent-add_p0'><code>chent$add_p0()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-chent-add_soil_degradation'><code>chent$add_soil_degradation()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-chent-add_soil_ff'><code>chent$add_soil_ff()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-chent-add_soil_sorption'><code>chent$add_soil_sorption()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-chent-add_transformation'><code>chent$add_transformation()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-chent-emf'><code>chent$emf()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-chent-get_chyaml'><code>chent$get_chyaml()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-chent-get_pubchem'><code>chent$get_pubchem()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-chent-get_rdkit'><code>chent$get_rdkit()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-chent-pdf'><code>chent$pdf()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-chent-png'><code>chent$png()</code></a></span></li> + <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-chent-try_pubchem'><code>chent$try_pubchem()</code></a></span></li> +</ul> +</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$new( +\if{html}{\out{<a id="method-pai-initialize"></a>}} +\if{latex}{\out{\hypertarget{method-pai-initialize}{}}} +\subsection{\code{pai$new()}}{ + Create a new pai object + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{pai$new( iso, identifier = iso, smiles = NULL, - smiles_source = "user", inchikey = NULL, - inchikey_source = "user", - alanwood = TRUE, + bcpc = TRUE, pubchem = TRUE, pubchem_from = "auto", rdkit = TRUE, template = NULL, - chyaml = TRUE -)}\if{html}{\out{</div>}} + chyaml = FALSE +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{iso}}{The ISO common name to be used in the query of the +BCPC compendium} + \item{\code{identifier}}{Alternative identifier used for querying pubchem} + \item{\code{smiles}}{Optional user provided SMILES code} + \item{\code{inchikey}}{Optional user provided InChI Key} + \item{\code{bcpc}}{Should the BCPC compendium be queried?} + \item{\code{pubchem}}{Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?} + \item{\code{pubchem_from}}{Possibility to select the argument +that is used to query pubchem} + \item{\code{rdkit}}{Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?} + \item{\code{template}}{An optional SMILES code to be used as template for RDKit} + \item{\code{chyaml}}{Should we look for a identifier.yaml file in the working} + } + \if{html}{\out{</div>}} + } } -} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-clone"></a>}} -\if{latex}{\out{\hypertarget{method-clone}{}}} -\subsection{Method \code{clone()}}{ -The objects of this class are cloneable with this method. -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{pai$clone(deep = FALSE)}\if{html}{\out{</div>}} +\if{html}{\out{<a id="method-pai-clone"></a>}} +\if{latex}{\out{\hypertarget{method-pai-clone}{}}} +\subsection{\code{pai$clone()}}{ + The objects of this class are cloneable with this method. + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{pai$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>}} + } } -\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 e5a8770..1ac1be6 100644 --- a/man/plot.chent.Rd +++ b/man/plot.chent.Rd @@ -9,8 +9,18 @@ \arguments{ \item{x}{The chent object to be plotted} -\item{...}{Further arguments passed to \code{\link{grid.picture}}} +\item{...}{Further arguments passed to \link[grImport:grid.picture]{grImport::grid.picture}} } \description{ Plot method for chent objects } +\examples{ +# Don't run examples per default, as PubChem may be unavailable +\dontrun{ +caffeine <- chent$new("caffeine") +print(caffeine) +if (!is.null(caffeine$Picture)) { + plot(caffeine) +} +} +} diff --git a/man/pp.Rd b/man/pp.Rd deleted file mode 100644 index cd950df..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-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>}} -} - -} -\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>}} -} -} -} diff --git a/man/ppp.Rd b/man/ppp.Rd new file mode 100644 index 0000000..9942b36 --- /dev/null +++ b/man/ppp.Rd @@ -0,0 +1,87 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/chent.R +\name{ppp} +\alias{ppp} +\title{R6 class for a plant protection product with at least one active ingredient} +\format{ +An \link[R6:R6Class]{R6::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} + } + \if{html}{\out{</div>}} +} +\section{Methods}{ +\subsection{Public methods}{ + \itemize{ + \item \href{#method-ppp-initialize}{\code{ppp$new()}} + \item \href{#method-ppp-clone}{\code{ppp$clone()}} + } +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-ppp-initialize"></a>}} +\if{latex}{\out{\hypertarget{method-ppp-initialize}{}}} +\subsection{\code{ppp$new()}}{ + Creates a new instance of this \link[R6:R6Class]{R6} class. + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{ppp$new( + name, + ..., + concentrations, + concentration_units = "g/L", + density = 1000, + density_units = "g/L" +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{name}}{The name of the product} + \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} + } + \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{\code{ppp$clone()}}{ + The objects of this class are cloneable with this method. + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{ppp$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>}} + } +} + +} diff --git a/man/print.ppp.Rd b/man/print.ppp.Rd new file mode 100644 index 0000000..553769b --- /dev/null +++ b/man/print.ppp.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/chent.R +\name{print.ppp} +\alias{print.ppp} +\title{Printing method for ppp objects (plant protection products)} +\usage{ +\method{print}{ppp}(x, ...) +} +\arguments{ +\item{x}{The chent object to be printed} + +\item{...}{Further arguments for compatibility with the S3 method} +} +\description{ +Printing method for ppp objects (plant protection products) +} |
