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Diffstat (limited to 'man')
| -rw-r--r-- | man/chent.Rd | 764 | ||||
| -rw-r--r-- | man/figures/README-unnamed-chunk-5-1.png | bin | 16259 -> 6180 bytes | |||
| -rw-r--r-- | man/figures/README-unnamed-chunk-6-1.png | bin | 0 -> 16259 bytes | |||
| -rw-r--r-- | man/pai.Rd | 145 | ||||
| -rw-r--r-- | man/ppp.Rd | 101 |
5 files changed, 484 insertions, 526 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index b348070..ca5f267 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -4,7 +4,7 @@ \alias{chent} \title{An R6 class for chemical entities with associated data} \format{ -An \link[R6:R6Class]{R6::R6Class} generator object +An \link[R6:R6Class]{R6Class} generator object } \description{ The class is initialised with an identifier. Chemical @@ -24,84 +24,85 @@ print(oct) } } \section{Public fields}{ -\if{html}{\out{<div class="r6-fields">}} -\describe{ -\item{\code{identifier}}{(\code{character(1)})\cr + \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}}{(\code{character(1)})\cr + \item{\code{inchikey}}{(\code{character(1)})\cr InChI Key, with attribute 'source'} -\item{\code{smiles}}{(\code{character()})\cr + \item{\code{smiles}}{(\code{character()})\cr SMILES code(s), with attribute 'source'} -\item{\code{mw}}{(\code{numeric(1)})\cr + \item{\code{mw}}{(\code{numeric(1)})\cr Molecular weight, with attribute 'source'} -\item{\code{pubchem}}{(\code{list()})\cr + \item{\code{pubchem}}{(\code{list()})\cr List of information retrieved from PubChem} -\item{\code{rdkit}}{List of information obtained with RDKit} + \item{\code{rdkit}}{List of information obtained with RDKit} -\item{\code{mol}}{<rdkit.Chem.rdchem.Mol> object} + \item{\code{mol}}{<rdkit.Chem.rdchem.Mol> object} -\item{\code{svg}}{SVG code} + \item{\code{svg}}{SVG code} -\item{\code{Picture}}{Graph as a \link[grImport:Picture-class]{grImport::Picture} object obtained using the grImport package} + \item{\code{Picture}}{Graph as a \link[grImport:Picture-class]{grImport::Picture} object obtained using the grImport package} -\item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file} + \item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file} -\item{\code{pdf_height}}{Height of the MediaBox in the pdf after cropping} + \item{\code{pdf_height}}{Height of the MediaBox in the pdf after cropping} -\item{\code{p0}}{Vapour pressure in Pa} + \item{\code{p0}}{Vapour pressure in Pa} -\item{\code{cwsat}}{Water solubility in mg/L} + \item{\code{cwsat}}{Water solubility in mg/L} -\item{\code{PUF}}{Plant uptake factor} + \item{\code{PUF}}{Plant uptake factor} -\item{\code{chyaml}}{List of information obtained from a YAML file} + \item{\code{chyaml}}{List of information obtained from a YAML file} -\item{\code{TPs}}{List of transformation products as chent objects} + \item{\code{TPs}}{List of transformation products as chent objects} -\item{\code{transformations}}{Data frame of observed transformations} + \item{\code{transformations}}{Data frame of observed transformations} -\item{\code{soil_degradation}}{Dataframe of modelling DT50 values} + \item{\code{soil_degradation}}{Dataframe of modelling DT50 values} -\item{\code{soil_ff}}{Dataframe of formation fractions} + \item{\code{soil_ff}}{Dataframe of formation fractions} -\item{\code{soil_sorption}}{Dataframe of soil sorption data} -} -\if{html}{\out{</div>}} + \item{\code{soil_sorption}}{Dataframe of soil sorption data} + } + \if{html}{\out{</div>}} } \section{Methods}{ \subsection{Public methods}{ -\itemize{ -\item \href{#method-chent-new}{\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$clone()}} -} + \itemize{ + \item \href{#method-chent-initialize}{\code{chent$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-chent-new"></a>}} -\if{latex}{\out{\hypertarget{method-chent-new}{}}} -\subsection{Method \code{new()}}{ -Creates a new instance of this \link[R6:R6Class]{R6} class. -\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, inchikey = NULL, @@ -110,258 +111,250 @@ Creates a new instance of this \link[R6:R6Class]{R6} class. rdkit = TRUE, template = NULL, 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 +)} + \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 + \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 + \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 + \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{</div>}} -} -} + \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-try_pubchem"></a>}} \if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} -\subsection{Method \code{try_pubchem()}}{ -Try to get chemical information from PubChem -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query = self$identifier, from = "name")}\if{html}{\out{</div>}} +\subsection{\code{chent$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>}} + } } -\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-chent-get_pubchem"></a>}} \if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}} -\subsection{Method \code{get_pubchem()}}{ -Get chemical information from PubChem for a known PubChem CID -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}} +\subsection{\code{chent$get_pubchem()}}{ + Get chemical information from PubChem for a known PubChem CID + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$get_pubchem(pubchem_cid)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{pubchem_cid}}{CID} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{pubchem_cid}}{CID} -} -\if{html}{\out{</div>}} -} -} \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-get_rdkit"></a>}} \if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} -\subsection{Method \code{get_rdkit()}}{ -Get chemical information from RDKit if available -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} +\subsection{\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>}} + } } -\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-chent-get_chyaml"></a>}} \if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}} -\subsection{Method \code{get_chyaml()}}{ -Obtain information from a YAML file -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{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>}} -} - -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{repo}}{Should the file be looked for in the current working +)} + \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>}} -} + \item{\code{chyaml}}{The filename to be looked for} + } + \if{html}{\out{</div>}} + } } + \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_p0"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} -\subsection{Method \code{add_p0()}}{ -Add a vapour pressure -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} +\subsection{\code{chent$add_p0()}}{ + Add a vapour pressure + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{p0}}{The vapour pressure in Pa} + \item{\code{T}}{Temperature} + \item{\code{source}}{An acronym specifying the source of the information} + \item{\code{page}}{The page from which the information was taken} + \item{\code{remark}}{A remark} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{p0}}{The vapour pressure in Pa} - -\item{\code{T}}{Temperature} - -\item{\code{source}}{An acronym specifying the source of the information} - -\item{\code{page}}{The page from which the information was taken} - -\item{\code{remark}}{A remark} -} -\if{html}{\out{</div>}} -} -} \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_cwsat"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}} -\subsection{Method \code{add_cwsat()}}{ -Add a water solubility -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} +\subsection{\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>}} + } } -\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-chent-add_PUF"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} -\subsection{Method \code{add_PUF()}}{ -Add a plant uptake factor -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF( +\subsection{\code{chent$add_PUF()}}{ + Add a plant uptake factor + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$add_PUF( PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value" -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{PUF}}{The plant uptake factor, a number between 0 and 1} + \item{\code{source}}{An acronym specifying the source of the information} + \item{\code{page}}{The page from which the information was taken} + \item{\code{remark}}{A remark} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{PUF}}{The plant uptake factor, a number between 0 and 1} - -\item{\code{source}}{An acronym specifying the source of the information} - -\item{\code{page}}{The page from which the information was taken} - -\item{\code{remark}}{A remark} -} -\if{html}{\out{</div>}} -} -} \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_TP"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_TP}{}}} -\subsection{Method \code{add_TP()}}{ -Add a transformation product to the internal list -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}} +\subsection{\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>}} + } } -\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-chent-add_transformation"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} -\subsection{Method \code{add_transformation()}}{ -Add a line in the internal dataframe holding observed transformations -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{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$add_transformation( study_type, TP_identifier, max_occurrence, remark = "", source = NA, pages = NA -)}\if{html}{\out{</div>}} -} - -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{study_type}}{A characterisation of the study type} - -\item{\code{TP_identifier}}{An identifier of one of the transformation products +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{study_type}}{A characterisation of the study type} + \item{\code{TP_identifier}}{An identifier of one of the transformation products in \code{self$TPs}} - -\item{\code{max_occurrence}}{The maximum observed occurrence of the + \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>}} -} + \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-chent-add_soil_degradation"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}} -\subsection{Method \code{add_soil_degradation()}}{ -Add a line in the internal dataframe holding modelling DT50 values -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_degradation( +\subsection{\code{chent$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, @@ -380,88 +373,70 @@ Add a line in the internal dataframe holding modelling DT50 values remark = "", source, page = NA -)}\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 +)} + \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 + \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 + \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>}} -} + \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>}} \if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} -\subsection{Method \code{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{\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>}} + } } -\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-chent-add_soil_sorption"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}} -\subsection{Method \code{add_soil_sorption()}}{ -Add soil sorption data -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{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, @@ -476,128 +451,119 @@ Add soil sorption data remark = "", source, page = NA -)}\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) +)} + \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>}} -} + \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-chent-pdf"></a>}} \if{latex}{\out{\hypertarget{method-chent-pdf}{}}} -\subsection{Method \code{pdf()}}{ -Write a PDF image of the structure -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{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$identifier, ".pdf"), dir = "structures/pdf", template = NULL -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{file}}{The file to write to} + \item{\code{dir}}{The directory to write the file to} + \item{\code{template}}{An optional SMILES code to be used as template for RDKit} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{file}}{The file to write to} - -\item{\code{dir}}{The directory to write the file to} - -\item{\code{template}}{An optional SMILES code to be used as template for RDKit} -} -\if{html}{\out{</div>}} -} -} \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-png"></a>}} \if{latex}{\out{\hypertarget{method-chent-png}{}}} -\subsection{Method \code{png()}}{ -Write a PNG image of the structure -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$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$identifier, ".png"), dir = "structures/png", antialias = "gray" -)}\if{html}{\out{</div>}} +)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{file}}{The file to write to} + \item{\code{dir}}{The directory to write the file to} + \item{\code{antialias}}{Passed to \link[grDevices:png]{png}} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{file}}{The file to write to} - -\item{\code{dir}}{The directory to write the file to} - -\item{\code{antialias}}{Passed to \link[grDevices:png]{png}} -} -\if{html}{\out{</div>}} -} -} \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-emf"></a>}} \if{latex}{\out{\hypertarget{method-chent-emf}{}}} -\subsection{Method \code{emf()}}{ -Write an EMF image of the structure using \link[devEMF:emf]{emf} -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}} +\subsection{\code{chent$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>}} + } } -\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-chent-clone"></a>}} \if{latex}{\out{\hypertarget{method-chent-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$clone(deep = FALSE)}\if{html}{\out{</div>}} +\subsection{\code{chent$clone()}}{ + The objects of this class are cloneable with this method. + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{chent$clone(deep = FALSE)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{deep}}{Whether to make a deep clone.} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{deep}}{Whether to make a deep clone.} -} -\if{html}{\out{</div>}} -} -} } diff --git a/man/figures/README-unnamed-chunk-5-1.png b/man/figures/README-unnamed-chunk-5-1.png Binary files differindex bf6cdb4..7e7352d 100644 --- a/man/figures/README-unnamed-chunk-5-1.png +++ b/man/figures/README-unnamed-chunk-5-1.png diff --git a/man/figures/README-unnamed-chunk-6-1.png b/man/figures/README-unnamed-chunk-6-1.png Binary files differnew file mode 100644 index 0000000..bf6cdb4 --- /dev/null +++ b/man/figures/README-unnamed-chunk-6-1.png @@ -27,53 +27,52 @@ print(decanol) } } \section{Super class}{ -\code{\link[chents:chent]{chents::chent}} -> \code{pai} +\code{\link[chents:chent]{chent}} -> \code{pai} } \section{Public fields}{ -\if{html}{\out{<div class="r6-fields">}} -\describe{ -\item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750} + \if{html}{\out{<div class="r6-fields">}} + \describe{ + \item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750} -\item{\code{bcpc}}{Information retrieved from the BCPC compendium available online + \item{\code{bcpc}}{Information retrieved from the BCPC compendium available online at <pesticidecompendium.bcpc.org>} -} -\if{html}{\out{</div>}} + } + \if{html}{\out{</div>}} } \section{Methods}{ \subsection{Public methods}{ -\itemize{ -\item \href{#method-pai-new}{\code{pai$new()}} -\item \href{#method-pai-clone}{\code{pai$clone()}} -} + \itemize{ + \item \href{#method-pai-initialize}{\code{pai$new()}} + \item \href{#method-pai-clone}{\code{pai$clone()}} + } } -\if{html}{\out{ -<details><summary>Inherited methods</summary> +\if{html}{\out{<details><summary>Inherited methods</summary> <ul> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-chent-add_PUF'><code>chents::chent$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>chents::chent$add_TP()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-chent-add_cwsat'><code>chents::chent$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>chents::chent$add_p0()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-chent-add_soil_degradation'><code>chents::chent$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>chents::chent$add_soil_ff()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-chent-add_soil_sorption'><code>chents::chent$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>chents::chent$add_transformation()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-chent-emf'><code>chents::chent$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>chents::chent$get_chyaml()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-chent-get_pubchem'><code>chents::chent$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>chents::chent$get_rdkit()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-chent-pdf'><code>chents::chent$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>chents::chent$png()</code></a></span></li> -<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-chent-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></li> + <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$try_pubchem()</code></a></span></li> </ul> -</details> -}} +</details>}} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-pai-new"></a>}} -\if{latex}{\out{\hypertarget{method-pai-new}{}}} -\subsection{Method \code{new()}}{ -Create a new pai object -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{pai$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, @@ -84,55 +83,49 @@ Create a new pai object rdkit = TRUE, template = NULL, 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 +)} + \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 + \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 + \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 + \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>}} -} + \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-pai-clone"></a>}} \if{latex}{\out{\hypertarget{method-pai-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$clone(deep = FALSE)}\if{html}{\out{</div>}} +\subsection{\code{pai$clone()}}{ + The objects of this class are cloneable with this method. + \subsection{Usage}{ + \if{html}{\out{<div class="r">}} + \preformatted{pai$clone(deep = FALSE)} + \if{html}{\out{</div>}} + } + \subsection{Arguments}{ + \if{html}{\out{<div class="arguments">}} + \describe{ + \item{\code{deep}}{Whether to make a deep clone.} + } + \if{html}{\out{</div>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{deep}}{Whether to make a deep clone.} -} -\if{html}{\out{</div>}} -} -} } @@ -11,78 +11,77 @@ Contains basic information about the active ingredients in the product } \section{Public fields}{ -\if{html}{\out{<div class="r6-fields">}} -\describe{ -\item{\code{name}}{The name of the product} + \if{html}{\out{<div class="r6-fields">}} + \describe{ + \item{\code{name}}{The name of the product} -\item{\code{ais}}{A list of active ingredients} + \item{\code{ais}}{A list of active ingredients} -\item{\code{concentrations}}{The concentration of the ais} + \item{\code{concentrations}}{The concentration of the ais} -\item{\code{concentration_units}}{Defaults to g/L} + \item{\code{concentration_units}}{Defaults to g/L} -\item{\code{density}}{The density of the product} + \item{\code{density}}{The density of the product} -\item{\code{density_units}}{Defaults to g/L} -} -\if{html}{\out{</div>}} + \item{\code{density_units}}{Defaults to g/L} + } + \if{html}{\out{</div>}} } \section{Methods}{ \subsection{Public methods}{ -\itemize{ -\item \href{#method-ppp-new}{\code{ppp$new()}} -\item \href{#method-ppp-clone}{\code{ppp$clone()}} -} + \itemize{ + \item \href{#method-ppp-initialize}{\code{ppp$new()}} + \item \href{#method-ppp-clone}{\code{ppp$clone()}} + } } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-ppp-new"></a>}} -\if{latex}{\out{\hypertarget{method-ppp-new}{}}} -\subsection{Method \code{new()}}{ -Creates a new instance of this \link[R6:R6Class]{R6} class. -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{ppp$new( +\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>}} +)} + \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>}} + } } -\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{Method \code{clone()}}{ -The objects of this class are cloneable with this method. -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{ppp$clone(deep = FALSE)}\if{html}{\out{</div>}} +\subsection{\code{ppp$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>}} + } } -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{deep}}{Whether to make a deep clone.} -} -\if{html}{\out{</div>}} -} -} } |
