diff options
Diffstat (limited to 'R/chent.R')
| -rw-r--r-- | R/chent.R | 19 |
1 files changed, 16 insertions, 3 deletions
@@ -102,7 +102,6 @@ chent <- R6Class("chent", #' @description #' Creates a new instance of this [R6][R6::R6Class] class. - #' initialize = function(identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), rdkit = TRUE, template = NULL, @@ -166,6 +165,7 @@ chent <- R6Class("chent", invisible(self) }, + #' @description #' Try to get chemical information from PubChem #' @param query Query string to be passed to [get_cid][webchem::get_cid] #' @param from Passed to [get_cid][webchem::get_cid] @@ -181,6 +181,7 @@ chent <- R6Class("chent", } }, + #' @description #' Get chemical information from PubChem for a known PubChem CID #' @param pubchem_cid CID get_pubchem = function(pubchem_cid) { @@ -274,6 +275,7 @@ chent <- R6Class("chent", unlink(c(xmlfile, psfile, svgfile)) }, + #' @description #' Obtain information from a YAML file #' @param repo Should the file be looked for in the current working #' directory, a local git repository under `~/git/chyaml`, or from @@ -310,6 +312,7 @@ chent <- R6Class("chent", } }, + #' @description #' Add a vapour pressure #' @param p0 The vapour pressure in Pa add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { @@ -320,6 +323,7 @@ chent <- R6Class("chent", attr(self$p0, "remark") <- remark }, + #' @description #' Add a water solubility #' @param cwsat The water solubility in mg/L add_cwsat = function(cwsat, T = NA, pH = NA, @@ -333,6 +337,7 @@ chent <- R6Class("chent", attr(self$cwsat, "remark") <- remark }, + #' @description #' Add a plant uptake factor #' @param PUF The plant uptake factor, a number between 0 and 1 add_PUF = function(PUF = 0, @@ -348,6 +353,7 @@ chent <- R6Class("chent", #' @field TPs List of transformation products as chent objects TPs = list(), + #' @description #' Add a transformation product to the internal list #' @param x A [chent] object, or an identifier to generate a [chent] object #' @param pubchem Should chemical information be obtained from PubChem? @@ -370,6 +376,7 @@ chent <- R6Class("chent", page = character(0), stringsAsFactors = FALSE), + #' @description #' Add a line in the internal dataframe holding observed transformations #' @param study_type A characterisation of the study type #' @param TP_identifier An identifier of one of the transformation products @@ -400,6 +407,7 @@ chent <- R6Class("chent", #' @field soil_degradation Dataframe of modelling DT50 values soil_degradation = NULL, + #' @description #' Add a line in the internal dataframe holding modelling DT50 values #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide #' fate modelling @@ -452,7 +460,8 @@ chent <- R6Class("chent", #' @field soil_ff Dataframe of formation fractions soil_ff = NULL, - # Add one or more formation fractions for degradation in soil + #' @description + #' Add one or more formation fractions for degradation in soil #' @param target The identifier(s) of the transformation product #' @param soils The soil name(s) in which the transformation was observed #' @param ff The formation fraction(s) @@ -478,6 +487,7 @@ chent <- R6Class("chent", #' @field soil_sorption Dataframe of soil sorption data soil_sorption = NULL, + #' @description #' Add soil sorption data #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1) #' or according to Freundlich @@ -535,6 +545,7 @@ chent <- R6Class("chent", self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line)) }, + #' @description #' Write a PNG image of the structure #' @param antialias Passed to [png][grDevices::png] png = function(file = paste0(self$identifier, ".png"), @@ -666,9 +677,10 @@ pai <- R6Class("pai", #' at <pesticidecompendium.bcpc.org> bcpc = NULL, + #' @description + #' Create a new pai object #' @param iso The ISO common name to be used in the query of the #' BCPC compendium - #' #' @param identifier Alternative identifier used for querying pubchem #' @param smiles Optional user provided SMILES code #' @param inchikey Optional user provided InChI Key @@ -786,6 +798,7 @@ ppp <- R6Class("ppp", #' @field density_units Defaults to g/L density_units = "g/L", + #' @description #' Creates a new instance of this [R6][R6::R6Class] class. #' @param name The name of the product #' @param ... Identifiers of the active ingredients |