diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/chent.Rd | 144 | ||||
| -rw-r--r-- | man/pai.Rd | 26 | ||||
| -rw-r--r-- | man/pp.Rd | 77 | ||||
| -rw-r--r-- | man/ppp.Rd | 100 |
4 files changed, 265 insertions, 82 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index e069938..686d6c7 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -73,7 +73,8 @@ Add a line in the internal dataframe holding modelling DT50 values} \item{\code{soil_ff}}{Dataframe of formation fractions} -\item{\code{soil_sorption}}{Dataframe of soil sorption data} +\item{\code{soil_sorption}}{Dataframe of soil sorption data +Add soil sorption data} } \if{html}{\out{</div>}} } @@ -214,7 +215,9 @@ Obtain information from a YAML file} \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). +the web (not implemented).} + +\item{\code{chyaml}}{The filename to be looked for Add a vapour pressure} } \if{html}{\out{</div>}} @@ -256,7 +259,17 @@ Add a water solubility} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{p0}}{The water solubility in mg/L +\item{\code{cwsat}}{The water solubility in mg/L} + +\item{\code{T}}{Temperature} + +\item{\code{pH}}{The 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} } \if{html}{\out{</div>}} @@ -279,6 +292,12 @@ Add a plant uptake factor} \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>}} } @@ -318,6 +337,26 @@ Add a plant uptake factor} )}\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 page 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>}} @@ -346,6 +385,50 @@ Add a plant uptake factor} )}\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-chent-add_soil_ff"></a>}} @@ -355,6 +438,17 @@ Add a plant uptake factor} \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)} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}} @@ -379,6 +473,23 @@ Add a plant uptake factor} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\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{perc_clay}}{The percentage of clay in the soil} + +\item{\code{CEC}}{The cation exchange capacity +Write a PDF image of the structure} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-pdf"></a>}} @@ -392,6 +503,18 @@ Add a plant uptake factor} )}\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}}{A template expressed as SMILES to use in RDKit +Write a PNG image of the structure} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-png"></a>}} @@ -405,6 +528,14 @@ Add a plant uptake factor} )}\if{html}{\out{</div>}} } +\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}} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-emf"></a>}} @@ -414,6 +545,13 @@ Add a plant uptake factor} \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} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-chent-clone"></a>}} @@ -8,6 +8,11 @@ An \code{\link{R6Class}} generator object } \description{ +An R6 class for pesticidal active ingredients and associated data + +An R6 class for pesticidal active ingredients and associated data +} +\details{ The class is initialised with an identifier which is generally an ISO common name. Additional chemical information is retrieved from the internet if available. } @@ -31,9 +36,11 @@ if (!is.null(atr$Picture)) { \section{Public fields}{ \if{html}{\out{<div class="r6-fields">}} \describe{ -\item{\code{iso}}{ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org} +\item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750} -\item{\code{bcpc}}{List of information retrieved from pesticidecompendium.bcpc.org} +\item{\code{bcpc}}{Information retrieved from the BCPC compendium available online +at <pesticidecompendium.bcpc.org> +Creates a new instance of this \link[R6:R6Class]{R6} class.} } \if{html}{\out{</div>}} } @@ -69,6 +76,11 @@ if (!is.null(atr$Picture)) { \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$new( iso, @@ -84,6 +96,16 @@ if (!is.null(atr$Picture)) { )}\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} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-pai-clone"></a>}} diff --git a/man/pp.Rd b/man/pp.Rd deleted file mode 100644 index 363f9ba..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-pp-new}{\code{pp$new()}} -\item \href{#method-pp-print}{\code{pp$print()}} -\item \href{#method-pp-clone}{\code{pp$clone()}} -} -} -\if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-pp-new"></a>}} -\if{latex}{\out{\hypertarget{method-pp-new}{}}} -\subsection{Method \code{new()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{pp$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-pp-print"></a>}} -\if{latex}{\out{\hypertarget{method-pp-print}{}}} -\subsection{Method \code{print()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{pp$print()}\if{html}{\out{</div>}} -} - -} -\if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-pp-clone"></a>}} -\if{latex}{\out{\hypertarget{method-pp-clone}{}}} -\subsection{Method \code{clone()}}{ -The objects of this class are cloneable with this method. -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{pp$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..c0d35f1 --- /dev/null +++ b/man/ppp.Rd @@ -0,0 +1,100 @@ +% 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} +\format{ +An \code{\link{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 +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>}} +} +\section{Methods}{ +\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$clone()}} +} +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-ppp-new"></a>}} +\if{latex}{\out{\hypertarget{method-ppp-new}{}}} +\subsection{Method \code{new()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{ppp$new( + name, + ..., + concentrations, + concentration_units = "g/L", + density = 1000, + density_units = "g/L" +)}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<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$print()}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-ppp-clone"></a>}} +\if{latex}{\out{\hypertarget{method-ppp-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{ppp$clone(deep = FALSE)}\if{html}{\out{</div>}} +} + +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{</div>}} +} +} +} |