diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/chent.Rd | 75 | ||||
| -rw-r--r-- | man/pai.Rd | 39 | ||||
| -rw-r--r-- | man/ppp.Rd | 42 | ||||
| -rw-r--r-- | man/print.ppp.Rd | 16 |
4 files changed, 111 insertions, 61 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index 686d6c7..6edc226 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -105,6 +105,8 @@ Add soil sorption data} \if{latex}{\out{\hypertarget{method-chent-new}{}}} \subsection{Method \code{new()}}{ Creates a new instance of this \link[R6:R6Class]{R6} class. + +Try to get chemical information from PubChem \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$new( identifier, @@ -114,7 +116,7 @@ Creates a new instance of this \link[R6:R6Class]{R6} class. pubchem_from = c("name", "smiles", "inchikey"), rdkit = TRUE, template = NULL, - chyaml = TRUE + chyaml = FALSE )}\if{html}{\out{</div>}} } @@ -140,8 +142,7 @@ and the reticulate package?} \item{\code{template}}{An optional SMILES code to be used as template for RDKit} \item{\code{chyaml}}{Should we look for a identifier.yaml file in the working -directory? -Try to get chemical information from PubChem} +directory?} } \if{html}{\out{</div>}} } @@ -176,8 +177,7 @@ Get chemical information from PubChem for a known PubChem CID} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{pubchem_cid}}{CID -Get chemical information from RDKit if available} +\item{\code{pubchem_cid}}{CID} } \if{html}{\out{</div>}} } @@ -186,6 +186,8 @@ Get chemical information from RDKit if available} \if{html}{\out{<a id="method-chent-get_rdkit"></a>}} \if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} \subsection{Method \code{get_rdkit()}}{ +Get chemical information from RDKit if available +Obtain information from a YAML file \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} } @@ -193,8 +195,7 @@ 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>}} } @@ -234,7 +235,8 @@ Add a vapour pressure} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{p0}}{The vapour pressure in Pa} +\item{\code{p0}}{The vapour pressure in Pa +Add a water solubility} \item{\code{T}}{Temperature} @@ -242,8 +244,7 @@ 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>}} } @@ -259,18 +260,18 @@ Add a water solubility} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{cwsat}}{The water solubility in mg/L} +\item{\code{cwsat}}{The water solubility in mg/L +Add a plant uptake factor} \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>}} } @@ -315,7 +316,7 @@ 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?} } @@ -353,7 +354,7 @@ 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>}} } @@ -446,6 +447,12 @@ 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>}} } @@ -476,6 +483,8 @@ 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 +492,25 @@ 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 +519,8 @@ 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 +Write a PNG image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$pdf( file = paste0(self$identifier, ".pdf"), @@ -510,8 +536,7 @@ 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>}} } @@ -531,8 +556,11 @@ 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 +569,7 @@ 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 +578,8 @@ 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$Picture)) { \item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750} \item{\code{bcpc}}{Information retrieved from the BCPC compendium available online -at <pesticidecompendium.bcpc.org> -Creates a new instance of this \link[R6:R6Class]{R6} class.} +at <pesticidecompendium.bcpc.org>} } \if{html}{\out{</div>}} } @@ -72,11 +72,6 @@ Creates a new instance of this \link[R6:R6Class]{R6} class.} \if{html}{\out{<a id="method-pai-new"></a>}} \if{latex}{\out{\hypertarget{method-pai-new}{}}} \subsection{Method \code{new()}}{ -This class is derived from \link{chent}. It makes it easy -to create a \link{chent} from the ISO common name of a pesticide active -ingredient, and additionally stores the ISO name as well as -the complete result of querying the BCPC compendium using -\link[webchem:bcpc_query]{bcpc_query}. \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{pai$new( iso, @@ -88,7 +83,7 @@ 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 +94,26 @@ 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} @@ -26,24 +25,6 @@ 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} } \if{html}{\out{</div>}} } @@ -51,7 +32,6 @@ 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$clone()}} } } @@ -70,15 +50,23 @@ Printing method} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{name}}{The name of the product} + +\item{\code{...}}{Identifiers of the active ingredients} + +\item{\code{concentrations}}{Concentrations of the active ingredients} + +\item{\code{concentration_units}}{Defaults to g/L} + +\item{\code{density}}{The density} + +\item{\code{density_units}}{Defaults to g/L} } -\if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-ppp-print"></a>}} -\if{latex}{\out{\hypertarget{method-ppp-print}{}}} -\subsection{Method \code{print()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{ppp$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) +} |