diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/chent.Rd | 103 | ||||
| -rw-r--r-- | man/pai.Rd | 40 | ||||
| -rw-r--r-- | man/ppp.Rd | 46 | ||||
| -rw-r--r-- | man/print.ppp.Rd | 16 |
4 files changed, 126 insertions, 79 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index 686d6c7..ba47feb 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -12,17 +12,13 @@ information is retrieved from the internet. Additionally, it can be generated using RDKit if RDKit and its python bindings are installed. } \examples{ -oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) -print(oct) -if (!is.null(oct$Picture)) { - plot(oct) -} - caffeine <- chent$new("caffeine") print(caffeine) if (!is.null(caffeine$Picture)) { plot(caffeine) } +oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) +print(oct) } \section{Public fields}{ \if{html}{\out{<div class="r6-fields">}} @@ -62,19 +58,15 @@ List of information retrieved from PubChem} \item{\code{chyaml}}{List of information obtained from a YAML file} -\item{\code{TPs}}{List of transformation products as chent objects -Add a transformation product to the internal list} +\item{\code{TPs}}{List of transformation products as chent objects} -\item{\code{transformations}}{Data frame of observed transformations -Add a line in the internal dataframe holding observed transformations} +\item{\code{transformations}}{Data frame of observed transformations} -\item{\code{soil_degradation}}{Dataframe of modelling DT50 values -Add a line in the internal dataframe holding modelling DT50 values} +\item{\code{soil_degradation}}{Dataframe of modelling DT50 values} \item{\code{soil_ff}}{Dataframe of formation fractions} -\item{\code{soil_sorption}}{Dataframe of soil sorption data -Add soil sorption data} +\item{\code{soil_sorption}}{Dataframe of soil sorption data} } \if{html}{\out{</div>}} } @@ -114,7 +106,7 @@ Creates a new instance of this \link[R6:R6Class]{R6} class. pubchem_from = c("name", "smiles", "inchikey"), rdkit = TRUE, template = NULL, - chyaml = TRUE + chyaml = FALSE )}\if{html}{\out{</div>}} } @@ -140,8 +132,7 @@ and the reticulate package?} \item{\code{template}}{An optional SMILES code to be used as template for RDKit} \item{\code{chyaml}}{Should we look for a identifier.yaml file in the working -directory? -Try to get chemical information from PubChem} +directory?} } \if{html}{\out{</div>}} } @@ -150,6 +141,7 @@ Try to get chemical information from PubChem} \if{html}{\out{<a id="method-chent-try_pubchem"></a>}} \if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} \subsection{Method \code{try_pubchem()}}{ +Try to get chemical information from PubChem \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}} } @@ -159,8 +151,7 @@ Try to get chemical information from PubChem} \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} -Get chemical information from PubChem for a known PubChem CID} +\item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid}} } \if{html}{\out{</div>}} } @@ -169,6 +160,7 @@ Get chemical information from PubChem for a known PubChem CID} \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$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}} } @@ -176,8 +168,7 @@ Get chemical information from PubChem for a known PubChem CID} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{pubchem_cid}}{CID -Get chemical information from RDKit if available} +\item{\code{pubchem_cid}}{CID} } \if{html}{\out{</div>}} } @@ -186,6 +177,7 @@ Get chemical information from RDKit if available} \if{html}{\out{<a id="method-chent-get_rdkit"></a>}} \if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} \subsection{Method \code{get_rdkit()}}{ +Get chemical information from RDKit if available \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} } @@ -193,8 +185,7 @@ Get chemical information from RDKit if available} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{template}}{Optional template specified as a SMILES code -Obtain information from a YAML file} +\item{\code{template}}{An optional SMILES code to be used as template for RDKit} } \if{html}{\out{</div>}} } @@ -203,6 +194,7 @@ Obtain information from a YAML file} \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$get_chyaml( repo = c("wd", "local", "web"), @@ -217,8 +209,7 @@ Obtain information from a YAML file} directory, a local git repository under \verb{~/git/chyaml}, or from the web (not implemented).} -\item{\code{chyaml}}{The filename to be looked for -Add a vapour pressure} +\item{\code{chyaml}}{The filename to be looked for} } \if{html}{\out{</div>}} } @@ -227,6 +218,7 @@ Add a vapour pressure} \if{html}{\out{<a id="method-chent-add_p0"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} \subsection{Method \code{add_p0()}}{ +Add a vapour pressure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } @@ -242,8 +234,7 @@ Add a vapour pressure} \item{\code{page}}{The page from which the information was taken} -\item{\code{remark}}{A remark -Add a water solubility} +\item{\code{remark}}{A remark} } \if{html}{\out{</div>}} } @@ -252,6 +243,7 @@ Add a water solubility} \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$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } @@ -263,14 +255,13 @@ Add a water solubility} \item{\code{T}}{Temperature} -\item{\code{pH}}{The pH value} +\item{\code{pH}}{pH value} \item{\code{source}}{An acronym specifying the source of the information} \item{\code{page}}{The page from which the information was taken} -\item{\code{remark}}{A remark -Add a plant uptake factor} +\item{\code{remark}}{A remark} } \if{html}{\out{</div>}} } @@ -279,6 +270,7 @@ Add a plant uptake factor} \if{html}{\out{<a id="method-chent-add_PUF"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} \subsection{Method \code{add_PUF()}}{ +Add a plant uptake factor \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF( PUF = 0, @@ -306,6 +298,7 @@ Add a plant uptake factor} \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$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}} } @@ -315,7 +308,7 @@ Add a plant uptake factor} \describe{ \item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object} -\item{\code{smiles}}{A SMILES code for defining a \link{chent} object} +\item{\code{smiles}}{Optional user provided SMILES code} \item{\code{pubchem}}{Should chemical information be obtained from PubChem?} } @@ -326,6 +319,7 @@ Add a plant uptake factor} \if{html}{\out{<a id="method-chent-add_transformation"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} \subsection{Method \code{add_transformation()}}{ +Add a line in the internal dataframe holding observed transformations \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_transformation( study_type, @@ -353,7 +347,7 @@ result from stochiometric transformation} \item{\code{source}}{An acronym specifying the source of the information} -\item{\code{pages}}{The page from which the information was taken} +\item{\code{pages}}{The pages from which the information was taken} } \if{html}{\out{</div>}} } @@ -362,6 +356,7 @@ result from stochiometric transformation} \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$add_soil_degradation( soils, @@ -434,6 +429,7 @@ the technical active ingredient} \if{html}{\out{<a id="method-chent-add_soil_ff"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} \subsection{Method \code{add_soil_ff()}}{ +Add one or more formation fractions for degradation in soil \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}} } @@ -446,6 +442,12 @@ the technical active ingredient} \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>}} } @@ -454,6 +456,7 @@ the technical active ingredient} \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$add_soil_sorption( soils, @@ -476,6 +479,8 @@ the technical active ingredient} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ +\item{\code{soils}}{Names of the soils} + \item{\code{Kf}}{The sorption constant in L/kg, either linear (then \code{N} is 1) or according to Freundlich} @@ -483,10 +488,25 @@ or according to Freundlich} \item{\code{N}}{The Freundlich exponent} +\item{\code{type}}{The soil type} + +\item{\code{pH_orig}}{The pH stated in the study} + +\item{\code{pH_medium}}{The medium in which this pH was measured} + +\item{\code{pH_H2O}}{The pH extrapolated to pure water} + +\item{\code{perc_OC}}{The percentage of organic carbon in the soil} + \item{\code{perc_clay}}{The percentage of clay in the soil} -\item{\code{CEC}}{The cation exchange capacity -Write a PDF image of the structure} +\item{\code{CEC}}{The cation exchange capacity} + +\item{\code{remark}}{A remark} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} } \if{html}{\out{</div>}} } @@ -495,6 +515,7 @@ Write a PDF image of the structure} \if{html}{\out{<a id="method-chent-pdf"></a>}} \if{latex}{\out{\hypertarget{method-chent-pdf}{}}} \subsection{Method \code{pdf()}}{ +Write a PDF image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$pdf( file = paste0(self$identifier, ".pdf"), @@ -510,8 +531,7 @@ Write a PDF image of the structure} \item{\code{dir}}{The directory to write the file to} -\item{\code{template}}{A template expressed as SMILES to use in RDKit -Write a PNG image of the structure} +\item{\code{template}}{An optional SMILES code to be used as template for RDKit} } \if{html}{\out{</div>}} } @@ -520,6 +540,7 @@ Write a PNG image of the structure} \if{html}{\out{<a id="method-chent-png"></a>}} \if{latex}{\out{\hypertarget{method-chent-png}{}}} \subsection{Method \code{png()}}{ +Write a PNG image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$png( file = paste0(self$identifier, ".png"), @@ -531,8 +552,11 @@ Write a PNG image of the structure} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{antialias}}{Passed to \link[grDevices:png]{png} -Write an EMF image of the structure using \link[devEMF:emf]{emf}} +\item{\code{file}}{The file to write to} + +\item{\code{dir}}{The directory to write the file to} + +\item{\code{antialias}}{Passed to \link[grDevices:png]{png}} } \if{html}{\out{</div>}} } @@ -541,6 +565,7 @@ Write an EMF image of the structure using \link[devEMF:emf]{emf}} \if{html}{\out{<a id="method-chent-emf"></a>}} \if{latex}{\out{\hypertarget{method-chent-emf}{}}} \subsection{Method \code{emf()}}{ +Write an EMF image of the structure using \link[devEMF:emf]{emf} \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}} } @@ -549,6 +574,8 @@ Write an EMF image of the structure using \link[devEMF:emf]{emf}} \if{html}{\out{<div class="arguments">}} \describe{ \item{\code{file}}{The file to write to} + +\item{\code{dir}}{The directory to write the file to} } \if{html}{\out{</div>}} } @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/chent.R -\docType{class} \name{pai} \alias{pai} \title{An R6 class for pesticidal active ingredients and associated data} @@ -8,9 +7,11 @@ An \code{\link{R6Class}} generator object } \description{ -The class is initialised with an identifier which is generally -an ISO common name. Additional chemical information is retrieved from the -internet if available. +This class is derived from \link{chent}. It makes it easy +to create a \link{chent} from the ISO common name of a pesticide active +ingredient, and additionally stores the ISO name as well as +the complete result of querying the BCPC compendium using +\link[webchem:bcpc_query]{bcpc_query}. } \examples{ # On Travis, we get a certificate validation error, @@ -35,8 +36,7 @@ if (!is.null(atr$Picture)) { \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 -at <pesticidecompendium.bcpc.org> -Creates a new instance of this \link[R6:R6Class]{R6} class.} +at <pesticidecompendium.bcpc.org>} } \if{html}{\out{</div>}} } @@ -72,11 +72,7 @@ Creates a new instance of this \link[R6:R6Class]{R6} class.} \if{html}{\out{<a id="method-pai-new"></a>}} \if{latex}{\out{\hypertarget{method-pai-new}{}}} \subsection{Method \code{new()}}{ -This class is derived from \link{chent}. It makes it easy -to create a \link{chent} from the ISO common name of a pesticide active -ingredient, and additionally stores the ISO name as well as -the complete result of querying the BCPC compendium using -\link[webchem:bcpc_query]{bcpc_query}. +Create a new pai object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{pai$new( iso, @@ -88,7 +84,7 @@ the complete result of querying the BCPC compendium using pubchem_from = "auto", rdkit = TRUE, template = NULL, - chyaml = TRUE + chyaml = FALSE )}\if{html}{\out{</div>}} } @@ -99,6 +95,26 @@ the complete result of querying the BCPC compendium using 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>}} } @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/chent.R -\docType{class} \name{ppp} \alias{ppp} \title{R6 class for a plant protection product with at least one active ingredient} @@ -24,26 +23,7 @@ product \item{\code{density}}{The density of the product} -\item{\code{density_units}}{Defaults to g/L -Creates a new instance of this \link[R6:R6Class]{R6} class.} - -\item{\code{...}}{Identifiers of the active ingredients} - -\item{\code{concentrations}}{Concentrations of the active ingredients} - -\item{\code{concentration_units}}{Defaults to g/L} - -\item{\code{density}}{The density} - -\item{\code{density_units}}{Defaults to g/L -Printing method} -} -\if{html}{\out{</div>}} -} -\section{Active bindings}{ -\if{html}{\out{<div class="r6-active-bindings">}} -\describe{ -\item{\code{...}}{Identifiers of the active ingredients} +\item{\code{density_units}}{Defaults to g/L} } \if{html}{\out{</div>}} } @@ -51,7 +31,6 @@ Printing method} \subsection{Public methods}{ \itemize{ \item \href{#method-ppp-new}{\code{ppp$new()}} -\item \href{#method-ppp-print}{\code{ppp$print()}} \item \href{#method-ppp-clone}{\code{ppp$clone()}} } } @@ -59,6 +38,7 @@ Printing method} \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$new( name, @@ -70,15 +50,23 @@ Printing method} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{name}}{The name of the product} + +\item{\code{...}}{Identifiers of the active ingredients} + +\item{\code{concentrations}}{Concentrations of the active ingredients} + +\item{\code{concentration_units}}{Defaults to g/L} + +\item{\code{density}}{The density} + +\item{\code{density_units}}{Defaults to g/L} } -\if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-ppp-print"></a>}} -\if{latex}{\out{\hypertarget{method-ppp-print}{}}} -\subsection{Method \code{print()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{ppp$print()}\if{html}{\out{</div>}} +\if{html}{\out{</div>}} } - } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-ppp-clone"></a>}} 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) +} |